I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 1 21:12:40 +14 2024 I: pbuilder-time-stamp: 1733037160 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gromacs_2024.4-1.dsc] I: copying [./gromacs_2024.4.orig-regressiontests.tar.gz] I: copying [./gromacs_2024.4.orig.tar.gz] I: copying [./gromacs_2024.4-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 2 00:32:09 2024 gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F gpgv: issuer "nbreen@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gromacs_2024.4-1.dsc: no acceptable signature found dpkg-source: info: extracting gromacs in gromacs-2024.4 dpkg-source: info: unpacking gromacs_2024.4.orig.tar.gz dpkg-source: info: unpacking gromacs_2024.4.orig-regressiontests.tar.gz dpkg-source: info: unpacking gromacs_2024.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying readme.patch dpkg-source: info: applying copyright-file.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying manual-local-mathjax.patch dpkg-source: info: applying mpi-tests-localhost.patch dpkg-source: info: applying manual-image-conversion.patch dpkg-source: info: applying disable-gmxtimingtests.patch dpkg-source: info: applying script-shebang-line.patch dpkg-source: info: applying add-support-for-loong64.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1219924/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 1 07:12 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1219924/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1219924/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=7e32636124c3455cb19d8268d6b05907 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1219924 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.n6DVrGMq/pbuilderrc_pYy1 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.n6DVrGMq/b2 --logfile b2/build.log gromacs_2024.4-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1219924/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: architecture-is-64-bit, bash-completion, chrpath, cmake (>= 3.13), debhelper-compat (= 13), dh-python, libblas-dev, libboost-dev, libfftw3-dev, libhwloc-dev, liblapack-dev, libmuparser-dev (>= 2.3.4), lsb-release, mpi-default-bin, mpi-default-dev, pkgconf, python3-dev, python3-mpi4py, python3-networkx, python3-numpy, python3-pybind11, python3-pytest, zlib1g-dev, doxygen, furo, ghostscript, graphicsmagick, graphviz, mscgen, python3-pygments, python3-sphinx, python3-sphinx-argparse, python3-sphinx-copybutton, python3-sphinx-inline-tabs, python3-sphinxcontrib.autoprogram, python3-sphinxcontrib.plantuml, rdfind, symlinks, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20087 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on bash-completion; however: Package bash-completion is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake (>= 3.13); however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhwloc-dev; however: Package libhwloc-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuparser-dev (>= 2.3.4); however: Package libmuparser-dev is not installed. pbuilder-satisfydepends-dummy depends on lsb-release; however: Package lsb-release is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-bin; however: Package mpi-default-bin is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-mpi4py; however: Package python3-mpi4py is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on furo; however: Package furo is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on graphicsmagick; however: Package graphicsmagick is not installed. pbuilder-satisfydepends-dummy depends on graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python3-pygments; however: Package python3-pygments is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-copybutton; however: Package python3-sphinx-copybutton is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-inline-tabs; however: Package python3-sphinx-inline-tabs is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.autoprogram; however: Package python3-sphinxcontrib.autoprogram is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.plantuml; however: Package python3-sphinxcontrib.plantuml is not installed. pbuilder-satisfydepends-dummy depends on rdfind; however: Package rdfind is not installed. pbuilder-satisfydepends-dummy depends on symlinks; however: Package symlinks is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: ant{a} ant-optional{a} architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bash-completion{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-lmodern{a} fonts-urw-base35{a} furo{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} ghostscript{a} graphicsmagick{a} graphviz{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} java-common{a} java-wrappers{a} libabsl20230802{a} libamd-comgr2{a} libamdhip64-5{a} libann0{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavalon-framework-java{a} libavif16{a} libbatik-java{a} libbcpkix-java{a} libbcprov-java{a} libbcutil-java{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcairo2{a} libcbor0.10{a} libcdt5{a} libcgraph6{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcommons-io-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontbox-java{a} libfontbox2-java{a} libfontconfig1{a} libfontenc1{a} libfop-java{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgd3{a} libgfortran-14-dev{a} libgfortran5{a} libgif7{a} libglib2.0-0t64{a} libgraphicsmagick-q16-3t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libgts-0.7-5t64{a} libgvc6{a} libgvpr2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libhwy1t64{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libimagequant0{a} libimath-3-1-29t64{a} libjakarta-servlet-api-java{a} libjaxp1.3-java{a} libjbig0{a} libjbig2dec0{a} libjlatexmath-java{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libjxl0.9{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} libllvm19{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libmunge2{a} libmuparser-dev{a} libmuparser2v5{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnsl2{a} libnspr4{a} libnss3{a} libnuma-dev{a} libnuma1{a} libopenexr-3-1-30{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi40{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpciaccess0{a} libpcsclite1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libpsl5t64{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqdox-java{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librhino-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsvtav1enc2{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libwebp7{a} libwebpmux3{a} libwmflite-0.2-7{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml-commons-external-java{a} libxml2{a} libxmlgraphics-commons-java{a} libxmu6{a} libxnvctrl0{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyuv0{a} libz3-4{a} libzzip-0-13t64{a} lsb-release{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} mscgen{a} netbase{a} ocl-icd-libopencl1{a} openjdk-21-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pkgconf{a} pkgconf-bin{a} plantuml{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} pybind11-dev{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-bs4{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-mpi4py{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybind11{a} python3-pygments{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-copybutton{a} python3-sphinx-inline-tabs{a} python3-sphinxcontrib.autoprogram{a} python3-sphinxcontrib.plantuml{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-basic-ng{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus default-jre dvisvgm fonts-droid-fallback fonts-liberation fonts-texgyre fonts-texgyre-math icc-profiles-free javascript-common krb5-locales libarchive-cpio-perl libasound2t64 libcoarrays-openmpi-dev libeigen3-dev libfile-mimeinfo-perl libglib2.0-data libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libldap-common libmail-sendmail-perl libnet-dbus-perl liboss4-salsa-asound2 libsasl2-modules libsaxon-java libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults lmodern lynx psmisc publicsuffix python3-gdal python3-lxml python3-matplotlib python3-pil python3-pydot python3-pygraphviz python3-scipy python3-yaml ruby shared-mime-info texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 366 newly installed, 0 to remove and 0 not upgraded. Need to get 440 MB of archives. After unpacking 1934 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-3 [808 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-3 [1940 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-3 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2~rc1-1 [23.5 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 13 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-3 [1902 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-3 [671 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 bash-completion all 1:2.14.0-2 [310 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 openssh-client arm64 1:9.9p1-3 [928 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 java-common all 0.76 [6776 B] Get: 47 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.106-1 [1292 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libpcsclite1 arm64 2.3.0-3 [55.1 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 openjdk-21-jre-headless arm64 21.0.5+11-1 [40.6 MB] Get: 53 http://deb.debian.org/debian unstable/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 54 http://deb.debian.org/debian unstable/main arm64 ant all 1.10.15-1 [2163 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 ant-optional all 1.10.15-1 [456 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 architecture-properties arm64 0.2.3 [2184 B] Get: 57 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.1-1 [2267 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.1-1 [9873 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 86 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 98 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libllvm19 arm64 1:19.1.4-1 [23.3 MB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libclang-cpp19 arm64 1:19.1.4-1 [12.0 MB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libclang1-19 arm64 1:19.1.4-1 [6865 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2+b3 [4515 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 119 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1+b1 [463 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 fonts-lmodern all 2.005-1 [4540 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 python3-bs4 all 4.12.3-3 [133 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 7.4.7-4 [731 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 python3-babel all 2.16.0-1 [114 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 138 http://deb.debian.org/debian unstable/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 142 http://deb.debian.org/debian unstable/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 python3-urllib3 all 2.2.3-3 [112 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 7.4.7-4 [588 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 sphinx-basic-ng all 1.0.0~beta2-1 [13.0 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 furo all 2024.08.06+dfsg-1 [62.8 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-9 [361 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libgfortran-14-dev arm64 14.2.0-9 [427 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-9 [9793 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 gfortran-14 arm64 14.2.0-9 [12.8 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libgs-common all 10.04.0~dfsg-2 [148 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libgs10-common all 10.04.0~dfsg-2 [475 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libavahi-common-data arm64 0.8-14 [112 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libavahi-common3 arm64 0.8-14 [43.0 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libdbus-1-3 arm64 1.14.10-6 [196 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libavahi-client3 arm64 0.8-14 [46.5 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libcups2t64 arm64 2.4.10-2 [235 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libidn12 arm64 1.42-2+b1 [80.2 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 libijs-0.35 arm64 0.35-15.1+b2 [14.9 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 libjbig2dec0 arm64 0.20-1+b3 [60.1 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b2 [13.0 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b1 [173 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 libgs10 arm64 10.04.0~dfsg-2 [2351 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 ghostscript arm64 10.04.0~dfsg-2 [50.7 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 libdav1d7 arm64 1.5.0-1+b1 [248 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-dav1d arm64 1.19.3-1 [11.2 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 libheif-plugin-libde265 arm64 1.19.3-1 [14.9 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 libheif1 arm64 1.19.3-1 [419 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 libhwy1t64 arm64 1.2.0-2+b1 [500 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 libimath-3-1-29t64 arm64 3.1.12-1+b1 [38.3 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 libopenexr-3-1-30 arm64 3.1.5-5.1+b3 [856 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 libjxl0.9 arm64 0.9.2-10+b1 [811 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 libwmflite-0.2-7 arm64 0.2.13-1.1+b3 [72.0 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 libgraphicsmagick-q16-3t64 arm64 1.4+really1.3.45-1+b1 [1078 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 graphicsmagick arm64 1.4+really1.3.45-1+b1 [1080 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 libann0 arm64 1.1.2+doc-9+b2 [24.1 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 libcdt5 arm64 2.42.4-2+b1 [39.4 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 libcgraph6 arm64 2.42.4-2+b1 [61.3 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 libaom3 arm64 3.11.0-1 [1690 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 libabsl20230802 arm64 20230802.1-4 [432 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 libgav1-1 arm64 0.19.0-2+b2 [493 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 librav1e0.7 arm64 0.7.1-7+b2 [653 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 libsvtav1enc2 arm64 2.2.1+dfsg-2 [1463 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 libyuv0 arm64 0.0.1898.20241125-1 [136 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 libavif16 arm64 1.1.1-1 [109 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 libxpm4 arm64 1:3.5.17-1+b2 [53.2 kB] Get: 215 http://deb.debian.org/debian unstable/main arm64 libgd3 arm64 2.3.3-12+b1 [115 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 libgts-0.7-5t64 arm64 0.7.6+darcs121130-5.2+b1 [145 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 221 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 222 http://deb.debian.org/debian unstable/main arm64 libltdl7 arm64 2.4.7-8 [392 kB] Get: 223 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 224 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 225 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 226 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [210 kB] Get: 227 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [51.8 kB] Get: 228 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [33.5 kB] Get: 229 http://deb.debian.org/debian unstable/main arm64 libpathplan4 arm64 2.42.4-2+b1 [41.4 kB] Get: 230 http://deb.debian.org/debian unstable/main arm64 libgvc6 arm64 2.42.4-2+b1 [628 kB] Get: 231 http://deb.debian.org/debian unstable/main arm64 libgvpr2 arm64 2.42.4-2+b1 [182 kB] Get: 232 http://deb.debian.org/debian unstable/main arm64 liblab-gamut1 arm64 2.42.4-2+b1 [198 kB] Get: 233 http://deb.debian.org/debian unstable/main arm64 libxmu6 arm64 2:1.1.3-3+b3 [55.6 kB] Get: 234 http://deb.debian.org/debian unstable/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB] Get: 235 http://deb.debian.org/debian unstable/main arm64 graphviz arm64 2.42.4-2+b1 [574 kB] Get: 236 http://deb.debian.org/debian unstable/main arm64 libnl-3-200 arm64 3.7.0-0.3+b1 [57.0 kB] Get: 237 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-200 arm64 3.7.0-0.3+b1 [167 kB] Get: 238 http://deb.debian.org/debian unstable/main arm64 libibverbs1 arm64 52.0-2+b1 [58.8 kB] Get: 239 http://deb.debian.org/debian unstable/main arm64 ibverbs-providers arm64 52.0-2+b1 [321 kB] Get: 240 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 241 http://deb.debian.org/debian unstable/main arm64 java-wrappers all 0.5 [8848 B] Get: 242 http://deb.debian.org/debian unstable/main arm64 libllvm17t64 arm64 1:17.0.6-18 [21.3 MB] Get: 243 http://deb.debian.org/debian unstable/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 244 http://deb.debian.org/debian unstable/main arm64 libdrm-common all 2.4.123-1 [8084 B] Get: 245 http://deb.debian.org/debian unstable/main arm64 libdrm2 arm64 2.4.123-1 [38.0 kB] Get: 246 http://deb.debian.org/debian unstable/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [21.6 kB] Get: 247 http://deb.debian.org/debian unstable/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 248 http://deb.debian.org/debian unstable/main arm64 libhsakmt1 arm64 6.1.2+ds-1 [56.9 kB] Get: 249 http://deb.debian.org/debian unstable/main arm64 libhsa-runtime64-1 arm64 6.1.2-2 [300 kB] Get: 250 http://deb.debian.org/debian unstable/main arm64 libamdhip64-5 arm64 5.7.1-5 [8823 kB] Get: 251 http://deb.debian.org/debian unstable/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 252 http://deb.debian.org/debian unstable/main arm64 libavalon-framework-java all 4.2.0+ds-1 [70.8 kB] Get: 253 http://deb.debian.org/debian unstable/main arm64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 254 http://deb.debian.org/debian unstable/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 255 http://deb.debian.org/debian unstable/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 256 http://deb.debian.org/debian unstable/main arm64 libcommons-io-java all 2.17.0-1 [488 kB] Get: 257 http://deb.debian.org/debian unstable/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 258 http://deb.debian.org/debian unstable/main arm64 libxmlgraphics-commons-java all 2.10-2 [628 kB] Get: 259 http://deb.debian.org/debian unstable/main arm64 librhino-java all 1.7.15-1 [1382 kB] Get: 260 http://deb.debian.org/debian unstable/main arm64 libbatik-java all 1.18+dfsg-2 [3940 kB] Get: 261 http://deb.debian.org/debian unstable/main arm64 libbcprov-java all 1.77-1 [5300 kB] Get: 262 http://deb.debian.org/debian unstable/main arm64 libbcutil-java all 1.77-1 [593 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 libbcpkix-java all 1.77-1 [956 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 265 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.0-4 [106 kB] Get: 266 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b2 [10.6 MB] Get: 267 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 268 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 269 http://deb.debian.org/debian unstable/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 270 http://deb.debian.org/debian unstable/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 271 http://deb.debian.org/debian unstable/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 272 http://deb.debian.org/debian unstable/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 273 http://deb.debian.org/debian unstable/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 274 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 275 http://deb.debian.org/debian unstable/main arm64 librdmacm1t64 arm64 52.0-2+b1 [67.4 kB] Get: 276 http://deb.debian.org/debian unstable/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 277 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get: 278 http://deb.debian.org/debian unstable/main arm64 libfftw3-long3 arm64 3.3.10-2+b1 [546 kB] Get: 279 http://deb.debian.org/debian unstable/main arm64 libfftw3-single3 arm64 3.3.10-2+b1 [517 kB] Get: 280 http://deb.debian.org/debian unstable/main arm64 libfftw3-bin arm64 3.3.10-2+b1 [44.3 kB] Get: 281 http://deb.debian.org/debian unstable/main arm64 libfftw3-dev arm64 3.3.10-2+b1 [1280 kB] Get: 282 http://deb.debian.org/debian unstable/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 283 http://deb.debian.org/debian unstable/main arm64 libfontbox2-java all 2.0.29-1 [1510 kB] Get: 284 http://deb.debian.org/debian unstable/main arm64 libqdox-java all 1.12.1-4 [173 kB] Get: 285 http://deb.debian.org/debian unstable/main arm64 libjakarta-servlet-api-java all 6.1.0-1 [376 kB] Get: 286 http://deb.debian.org/debian unstable/main arm64 libfop-java all 1:2.10+dfsg-1 [4588 kB] Get: 287 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB] Get: 288 http://deb.debian.org/debian unstable/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB] Get: 289 http://deb.debian.org/debian unstable/main arm64 libltdl-dev arm64 2.4.7-8 [165 kB] Get: 290 http://deb.debian.org/debian unstable/main arm64 libhwloc-dev arm64 2.11.2-1 [237 kB] Get: 291 http://deb.debian.org/debian unstable/main arm64 libpciaccess0 arm64 0.17-3+b2 [51.2 kB] Get: 292 http://deb.debian.org/debian unstable/main arm64 libxnvctrl0 arm64 535.171.04-1+b1 [14.1 kB] Get: 293 http://deb.debian.org/debian unstable/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b2 [39.3 kB] Get: 294 http://deb.debian.org/debian unstable/main arm64 libhwloc-plugins arm64 2.11.2-1 [17.9 kB] Get: 295 http://deb.debian.org/debian unstable/main arm64 libibumad3 arm64 52.0-2+b1 [27.1 kB] Get: 296 http://deb.debian.org/debian unstable/main arm64 libibmad5 arm64 52.0-2+b1 [41.5 kB] Get: 297 http://deb.debian.org/debian unstable/main arm64 libnl-3-dev arm64 3.7.0-0.3+b1 [101 kB] Get: 298 http://deb.debian.org/debian unstable/main arm64 libnl-route-3-dev arm64 3.7.0-0.3+b1 [198 kB] Get: 299 http://deb.debian.org/debian unstable/main arm64 libibverbs-dev arm64 52.0-2+b1 [625 kB] Get: 300 http://deb.debian.org/debian unstable/main arm64 libjlatexmath-java all 1.0.7-3 [995 kB] Get: 301 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 302 http://deb.debian.org/debian unstable/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5 [153 kB] Get: 303 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 304 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.0-4 [3709 kB] Get: 305 http://deb.debian.org/debian unstable/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB] Get: 306 http://deb.debian.org/debian unstable/main arm64 libmunge2 arm64 0.5.15-4+b1 [19.4 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 libmuparser2v5 arm64 2.3.4-1+b1 [127 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 libmuparser-dev arm64 2.3.4-1+b1 [33.5 kB] Get: 309 http://deb.debian.org/debian unstable/main arm64 libpmix2t64 arm64 5.0.4-1 [586 kB] Get: 310 http://deb.debian.org/debian unstable/main arm64 libucx0 arm64 1.17.0+ds-3 [959 kB] Get: 311 http://deb.debian.org/debian unstable/main arm64 libopenmpi40 arm64 5.0.6-2 [2083 kB] Get: 312 http://deb.debian.org/debian unstable/main arm64 openmpi-common all 5.0.6-2 [97.2 kB] Get: 313 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 314 http://deb.debian.org/debian unstable/main arm64 libpmix-dev arm64 5.0.4-1 [3942 kB] Get: 315 http://deb.debian.org/debian unstable/main arm64 openmpi-bin arm64 5.0.6-2 [180 kB] Get: 316 http://deb.debian.org/debian unstable/main arm64 libopenmpi-dev arm64 5.0.6-2 [1088 kB] Get: 317 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b2 [9128 B] Get: 318 http://deb.debian.org/debian unstable/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 319 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 320 http://deb.debian.org/debian unstable/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB] Get: 321 http://deb.debian.org/debian unstable/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5 [47.9 kB] Get: 322 http://deb.debian.org/debian unstable/main arm64 libpython3.12t64 arm64 3.12.7-3 [1982 kB] Get: 323 http://deb.debian.org/debian unstable/main arm64 libpython3.12-dev arm64 3.12.7-3 [4792 kB] Get: 324 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.12.7-1 [9980 B] Get: 325 http://deb.debian.org/debian unstable/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5 [60.3 kB] Get: 326 http://deb.debian.org/debian unstable/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB] Get: 327 http://deb.debian.org/debian unstable/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5 [106 kB] Get: 328 http://deb.debian.org/debian unstable/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 329 http://deb.debian.org/debian unstable/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB] Get: 330 http://deb.debian.org/debian unstable/main arm64 lsb-release all 12.1-1 [5912 B] Get: 331 http://deb.debian.org/debian unstable/main arm64 mpi-default-bin arm64 1.17 [2372 B] Get: 332 http://deb.debian.org/debian unstable/main arm64 mpi-default-dev arm64 1.17 [3148 B] Get: 333 http://deb.debian.org/debian unstable/main arm64 mscgen arm64 0.20-16 [45.1 kB] Get: 334 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 335 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 336 http://deb.debian.org/debian unstable/main arm64 plantuml all 1:1.2020.2+ds-5 [8132 kB] Get: 337 http://deb.debian.org/debian unstable/main arm64 tex-common all 6.18 [32.5 kB] Get: 338 http://deb.debian.org/debian unstable/main arm64 preview-latex-style all 13.2-1 [350 kB] Get: 339 http://deb.debian.org/debian unstable/main arm64 pybind11-dev all 2.13.6-1 [204 kB] Get: 340 http://deb.debian.org/debian unstable/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] Get: 341 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.12.7-1 [26.1 kB] Get: 342 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 343 http://deb.debian.org/debian unstable/main arm64 python3-mpi4py arm64 4.0.1-6+b1 [806 kB] Get: 344 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 345 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 346 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 347 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.13.6-1 [215 kB] Get: 348 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 349 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.16.0-7 [16.4 kB] Get: 350 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 351 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-copybutton all 0.5.2-2 [17.9 kB] Get: 352 http://deb.debian.org/debian unstable/main arm64 python3-sphinx-inline-tabs all 2023.4.21-1 [35.9 kB] Get: 353 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.autoprogram all 0.1.9-1 [10.6 kB] Get: 354 http://deb.debian.org/debian unstable/main arm64 python3-sphinxcontrib.plantuml all 0.5-8 [7992 B] Get: 355 http://deb.debian.org/debian unstable/main arm64 rdfind arm64 1.6.0-1+b2 [39.1 kB] Get: 356 http://deb.debian.org/debian unstable/main arm64 symlinks arm64 1.4-4+b1 [9992 B] Get: 357 http://deb.debian.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get: 358 http://deb.debian.org/debian unstable/main arm64 tex-gyre all 20180621-6 [6209 kB] Get: 359 http://deb.debian.org/debian unstable/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5 [7358 kB] Get: 360 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 361 http://deb.debian.org/debian unstable/main arm64 texlive-base all 2024.20241115-1 [22.7 MB] Get: 362 http://deb.debian.org/debian unstable/main arm64 texlive-fonts-recommended all 2024.20241115-1 [4991 kB] Get: 363 http://deb.debian.org/debian unstable/main arm64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get: 364 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 365 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 366 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] Fetched 440 MB in 3s (136 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package poppler-data. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... Selecting previously unselected package libexpat1:arm64. 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Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:arm64 (20230802.1-4) ... Setting up libgts-0.7-5t64:arm64 (0.7.6+darcs121130-5.2+b1) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.31.1-1) ... Setting up librhash1:arm64 (1.4.5-1) ... Setting up libcdt5:arm64 (2.42.4-2+b1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libcgraph6:arm64 (2.42.4-2+b1) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libjlatexmath-java (1.0.7-3) ... Setting up libevent-core-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libmuparser2v5:arm64 (2.3.4-1+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up lsb-release (12.1-1) ... Setting up libjaxp1.3-java (1.3.05-6) ... Setting up libfido2-1:arm64 (1.15.0-1+b1) ... Setting up libde265-0:arm64 (1.0.15-1+b2) ... Setting up libbcpkix-java (1.77-1) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:arm64 (1.4.0-0.1+b1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libyuv0:arm64 (0.0.1898.20241125-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libfmt10:arm64 (10.1.1+ds1-4) ... Setting up chrpath (0.18-1) ... Setting up libblas-dev:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsynctex2:arm64 (2024.20240313.70630+ds-5) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:arm64 (1.16-2+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-9) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libmuparser-dev:arm64 (2.3.4-1+b1) ... Setting up libllvm19:arm64 (1:19.1.4-1) ... Setting up libice6:arm64 (2:1.1.1-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up java-wrappers (0.5) ... Setting up libclang1-19 (1:19.1.4-1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxpm4:arm64 (1:3.5.17-1+b2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-14) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up libnss3:arm64 (2:3.106-1) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:arm64 (535.171.04-1+b1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-8) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:arm64 (2024.20240313.70630+ds-5) ... Setting up libllvm17t64:arm64 (1:17.0.6-18) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libopenexr-3-1-30:arm64 (3.1.5-5.1+b3) ... Setting up liblapack-dev:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libgav1-1:arm64 (0.19.0-2+b2) ... Setting up ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libgvpr2:arm64 (2.42.4-2+b1) ... Setting up libdrm2:arm64 (2.4.123-1) ... Setting up libnl-3-dev:arm64 (3.7.0-0.3+b1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-9) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libhwloc-dev:arm64 (2.11.2-1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up gfortran-14 (14.2.0-9) ... Setting up libsm6:arm64 (2:1.2.4-1) ... Setting up libarchive13t64:arm64 (3.7.4-1.1) ... Setting up libfftw3-dev:arm64 (3.3.10-2+b1) ... Setting up libavahi-client3:arm64 (0.8-14) ... Setting up libclang-cpp19 (1:19.1.4-1) ... Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... Setting up libpaper1:arm64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up libibverbs1:arm64 (52.0-2+b1) ... Setting up libavif16:arm64 (1.1.1-1) ... Setting up openjdk-21-jre-headless:arm64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libcurl4t64:arm64 (8.11.0-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up ibverbs-providers:arm64 (52.0-2+b1) ... Setting up libcommons-io-java (2.17.0-1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjxl0.9:arm64 (0.9.2-10+b1) ... Setting up libxmlgraphics-commons-java (2.10-2) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libhwloc-plugins:arm64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:arm64 (3.7.0-0.3+b1) ... Setting up doxygen (1.9.8+ds-2+b3) ... Setting up libraqm0:arm64 (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2+b1) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:arm64 (5.0.4-1) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up cmake (3.31.1-1) ... Setting up librdmacm1t64:arm64 (52.0-2+b1) ... Setting up libcups2t64:arm64 (2.4.10-2) ... Setting up tex-gyre (20180621-6) ... Setting up libhsakmt1:arm64 (6.1.2+ds-1) ... Setting up libfabric1:arm64 (1.17.0-3.1) ... Setting up libxmu6:arm64 (2:1.1.3-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-3) ... Setting up libbatik-java (1.18+dfsg-2) ... Setting up preview-latex-style (13.2-1) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libxaw7:arm64 (2:1.0.16-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libibverbs-dev:arm64 (52.0-2+b1) ... Setting up libpython3.12t64:arm64 (3.12.7-3) ... Setting up libhsa-runtime64-1:arm64 (6.1.2-2) ... Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up libgs10-common (10.04.0~dfsg-2) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up python3 (3.12.7-1) ... Setting up libpython3.12-dev:arm64 (3.12.7-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up python3-six (1.16.0-7) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.7-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.2.3-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up python3-soupsieve (2.6-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up libgs10:arm64 (10.04.0~dfsg-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libucx0:arm64 (1.17.0+ds-3) ... Setting up libpython3-dev:arm64 (3.12.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up libpango-1.0-0:arm64 (1.54.0+ds-3) ... Setting up python3-typeguard (4.4.1-1) ... Setting up ghostscript (10.04.0~dfsg-2) ... Setting up pybind11-dev (2.13.6-1) ... Setting up libcairo2:arm64 (1.18.2-2) ... Setting up python3-bs4 (4.12.3-3) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.7-1) ... Setting up texlive-binaries (2024.20240313.70630+ds-5) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ... Setting up texlive-base (2024.20241115-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-pybind11 (2.13.6-1) ... Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up libopenmpi40:arm64 (5.0.6-2) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-networkx (3.2.1-5) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up texlive-latex-base (2024.20241115-1) ... Setting up texlive-latex-recommended (2024.20241115-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up texlive-pictures (2024.20241115-1) ... Setting up texlive-fonts-recommended (2024.20241115-1) ... Setting up openmpi-bin (5.0.6-2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up dh-python (6.20241024) ... Setting up mpi-default-bin (1.17) ... Setting up texlive-latex-extra (2024.20241115-1) ... Setting up python3-mpi4py (4.0.1-6+b1) ... Setting up libheif-plugin-dav1d:arm64 (1.19.3-1) ... Setting up libheif-plugin-libde265:arm64 (1.19.3-1) ... Setting up libheif1:arm64 (1.19.3-1) ... Setting up libgd3:arm64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b1) ... Setting up graphviz (2.42.4-2+b1) ... Setting up libgraphicsmagick-q16-3t64 (1.4+really1.3.45-1+b1) ... Setting up mscgen (0.20-16) ... Setting up graphicsmagick (1.4+really1.3.45-1+b1) ... Processing triggers for libc-bin (2.40-4) ... ldconfig: Cannot mmap file /lib/aarch64-linux-gnu/libprrte.so. Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up ant (1.10.15-1) ... Setting up default-jre-headless (2:1.21-76) ... Setting up ant-optional (1.10.15-1) ... Setting up libfop-java (1:2.10+dfsg-1) ... Setting up plantuml (1:1.2020.2+ds-5) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (7.4.7-4) ... Setting up libpmix-dev:arm64 (5.0.4-1) ... Setting up python3-sphinx-copybutton (0.5.2-2) ... Setting up python3-sphinxcontrib.plantuml (0.5-8) ... Setting up python3-sphinx-argparse (0.5.2-1) ... Setting up sphinx-basic-ng (1.0.0~beta2-1) ... Setting up python3-sphinx-inline-tabs (2023.4.21-1) ... Setting up python3-sphinxcontrib.autoprogram (0.1.9-1) ... Setting up libopenmpi-dev:arm64 (5.0.6-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up furo (2024.08.06+dfsg-1) ... Setting up mpi-default-dev (1.17) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1219924/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1219924/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/gromacs-2024.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gromacs_2024.4-1_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2024.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nicholas Breen dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh_testdir dh_testroot dh_clean build-basic build-mpi build-manual build/ py3clean admin docs debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake \ /build/reproducible-path/gromacs-2024.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_INSTALL_LEGACY_API=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Using default binary suffix: "" -- Using default library suffix: "" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Configuring done (76.7s) -- Generating done (2.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake \ /build/reproducible-path/gromacs-2024.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Configuring done (87.4s) -- Generating done (2.8s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/basic-dp (mkdir -p build/mpi; cd build/mpi; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2024.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMXAPI=ON -DGMX_PYTHON_PACKAGE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.6 -- Using default binary suffix: "_mpi" -- Using default library suffix: "_mpi" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmx_mpi from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Configuring done (94.7s) -- Generating done (3.7s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/mpi (mkdir -p build/mpi-dp; cd build/mpi-dp; CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx cmake \ /build/reproducible-path/gromacs-2024.4 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_USE_MUPARSER=EXTERNAL -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_HWLOC=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DMPIEXEC="/usr/bin/mpiexec" -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Found MPI_CXX: /usr/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- GROMACS library will use OpenMPI 5.0.6 -- Using default binary suffix: "_mpi_d" -- Using default library suffix: "_mpi_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "2.11.0", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test C_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS -- Performing Test CXX_COMPILE_WORKS_WITHOUT_SPECIAL_FLAGS - Success -- Enabling ARM (AArch64) NEON Advanced SIMD instructions using CXX flags: -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_vsx in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so -- Looking for fftw_have_altivec in /usr/lib/aarch64-linux-gnu/libfftw3.so - not found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Configuring done (85.9s) -- Generating done (3.1s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/mpi-dp touch configure-stamp dh_testdir /usr/bin/make -j12 -C build/basic make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/basic//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/errhandler.cpp /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwlzh.c cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwt.c make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build cd 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc3.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 1%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include 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CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/basicoptions.cpp.o -MF CMakeFiles/options.dir/basicoptions.cpp.o.d -o CMakeFiles/options.dir/basicoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoptionmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 1%] Built target energyanalysis /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 5%] Built target thread_mpi cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull.cpp cd 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src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/nr_jacobi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/nr_jacobi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling && /usr/bin/c++ 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/transformationcoordinate.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 13%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment && 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/computeglobalselement.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 18%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/exceptions.cpp In file included from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:87: /build/reproducible-path/gromacs-2024.4/build/basic/src/include/buildinfo.h:73:9: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.11.0" | ^~~~~~~~~~~~~ In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:62: /usr/include/aarch64-linux-gnu/hwloc/autogen/config.h:15:9: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.11.2" | ^~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/niceheader.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/path.cpp.o -MF CMakeFiles/libgromacs.dir/utility/path.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistparams.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistset.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o 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CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/seed.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o 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CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -MF CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/calcgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -MF CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/share/template /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/share/template /build/reproducible-path/gromacs-2024.4/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/molecules.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 92%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp 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/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. 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/build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 96%] Built target gmxapi cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 98%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/argon-forces-integration.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/methane-water-integration.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/basic/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 98%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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'/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -j12 -C build/basic-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/basic-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp 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src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix 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&& /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/lmfit/lmmin.cpp /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/eigensolver.cpp [ 0%] Built target release-version-info /usr/bin/make -f 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src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/widemuldiv.c /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/mdrun.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/topology.cpp [ 0%] Built target energyanalysis /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/list.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsection.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 0%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 3%] Built target thread_mpi cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 3%] Built target scanner cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_angles.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 5%] Built target options cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_combination.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 7%] Built target tng_io_obj cd 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src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvardeps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvardeps.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvargrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvargrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarmodule.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 9%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/basic-dp 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarscript_commands.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarscript_commands_bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarscript_commands_bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment && 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -MF CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o.d -o CMakeFiles/modularsimulator.dir/freeenergyperturbationdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 13%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -MF CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o.d -o CMakeFiles/modularsimulator.dir/simulatoralgorithm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/simulatoralgorithm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 15%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/exceptions.cpp In file included from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:87: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include/buildinfo.h:73:9: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.11.0" | ^~~~~~~~~~~~~ In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:62: /usr/include/aarch64-linux-gnu/hwloc/autogen/config.h:15:9: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.11.2" | ^~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -MF CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/int64_to_int.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetree.cpp cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreemdpwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/smalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlineinit.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/cmdlinemodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/optimization.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/veccompare.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/vecdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/com.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/cubicsplinetable.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/forcetable.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/quadraticsplinetable.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atomprop.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/symtab.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/topsort.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/energyframe.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_analyze.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_saltbr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sans.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/nsfactor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/powerspect.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/pp2shift.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/solvate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/specbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/ter_db.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tomorse.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/topdirs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/topio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/toppush.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/topshake.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/toputil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/autocorr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -MF 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -MF CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -MF CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -MF CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/report_methods.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/force.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o 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CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biaswriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biaswriter.cpp cd 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/coordstate.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationgrid.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmforceprovider_stub.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarsMDModule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarsMDModule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/colvars/colvarproxygromacs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/disre.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/nvshmem_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/shellfc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/timecontrol.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/basic-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.9 -o ../../lib/libgromacs_d.so.9.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -lmuparser cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.9.0.0 ../../lib/libgromacs_d.so.9 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/resourceassignment.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/context.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/exceptions.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/box.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/interactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 94%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../lib/libgmxapi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_d.so.0.4.0 ../../lib/libgmxapi_d.so.0 ../../lib/libgmxapi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 96%] Built target gmxapi cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 98%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples 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api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/methane-water-integration.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples && /usr/bin/c++ -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 98%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/methane-water-integration.dir/link.d "CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o" -o ../../../bin/methane-water-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/basic-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -j12 -C build/basic tests make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles 74 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googletest 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Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend [ 2%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" [ 5%] Built 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Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 5%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 64%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic 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"--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 67%] Built target argon-forces-integration [ 68%] Built target methane-water-integration cd /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 68%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make 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-Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 68%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/testutils /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxlib/nonbonded/tests/CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -MF CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o.d -o CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/terminationhelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem 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CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/ebin.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energyoutput.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/booltype.cpp.o -MF CMakeFiles/utility-test.dir/booltype.cpp.o.d -o CMakeFiles/utility-test.dir/booltype.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include 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src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -MF CMakeFiles/applied_forces-test.dir/electricfield.cpp.o.d -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests/electricfield.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settle.cpp.o -MF CMakeFiles/mdlib-test.dir/settle.cpp.o.d -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target testutils-test /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settletestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include 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src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/applied_forces-test.dir/link.d "CMakeFiles/applied_forces-test.dir/electricfield.cpp.o" "CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target applied_forces-test /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests 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src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroups.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroups.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -MF CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o.d -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/updategroupscog.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 70%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/mock_helptopic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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"CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 72%] Built target mdlib-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/haloexchange_mpi.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 72%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmebsplinetest.cpp /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, LJCombinationRule)': /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:186:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 186 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/message_string_collector.cpp.o -MF CMakeFiles/utility-test.dir/message_string_collector.cpp.o.d -o CMakeFiles/utility-test.dir/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/message_string_collector.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 72%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 74%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 74%] Built target nbnxm-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -MF CMakeFiles/hardware-test.dir/cpuinfo.cpp.o.d -o CMakeFiles/hardware-test.dir/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/cpuinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 74%] Built target domdec-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" 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-I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 75%] Built target fft-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -MF CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o.d -o CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 75%] Built target listed_forces-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 75%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd 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../../../../../lib/libgromacs.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 77%] Built target awh-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests 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"CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target utility-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/gausstransform.cpp.o -MF CMakeFiles/math-test.dir/gausstransform.cpp.o.d -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target mdspan-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target ewald-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering 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cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target hardware-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o 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cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -MF CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o.d -o CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/normaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/timing-test.dir/link.d "CMakeFiles/timing-test.dir/timing.cpp.o" "CMakeFiles/timing-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/timing-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target timing-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/atoms.cpp.o -MF CMakeFiles/topology-test.dir/atoms.cpp.o.d -o CMakeFiles/topology-test.dir/atoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/filenameoptionmanager.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o ../CMakeFiles/taskassignment.dir/resourcedivision.cpp.o ../CMakeFiles/taskassignment.dir/taskassignment.cpp.o ../CMakeFiles/taskassignment.dir/usergpuids.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 78%] Built target taskassignment-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/base.cpp.o -MF CMakeFiles/simd-test.dir/base.cpp.o.d -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/base.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar.cpp.o -MF CMakeFiles/simd-test.dir/scalar.cpp.o.d -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -MF CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] Built target pbcutil-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests /build/reproducible-path/gromacs-2024.4/build/basic 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-O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] Built target pull-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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-O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_chi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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/build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genion.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] Built target mdtypes-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 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cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem 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-o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_memory.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pdb2gmx2-test.dir/link.d "CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] Built target pdb2gmx2-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/datatest.cpp /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp:169:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 169 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/mock_datamodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -MF CMakeFiles/correlations-test.dir/correlationdataset.cpp.o.d -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/correlationdataset.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 79%] 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/builder.cpp.o -MF CMakeFiles/coordinateio-test.dir/builder.cpp.o.d -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/builder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/math-test.dir/link.d "CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o" "CMakeFiles/math-test.dir/boxmatrix.cpp.o" "CMakeFiles/math-test.dir/coordinatetransformation.cpp.o" "CMakeFiles/math-test.dir/densityfit.cpp.o" "CMakeFiles/math-test.dir/dofit.cpp.o" "CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o" "CMakeFiles/math-test.dir/functions.cpp.o" "CMakeFiles/math-test.dir/gausstransform.cpp.o" "CMakeFiles/math-test.dir/densityfittingforce.cpp.o" "CMakeFiles/math-test.dir/invertmatrix.cpp.o" "CMakeFiles/math-test.dir/matrix.cpp.o" "CMakeFiles/math-test.dir/multidimarray.cpp.o" "CMakeFiles/math-test.dir/neldermead.cpp.o" "CMakeFiles/math-test.dir/optimization.cpp.o" "CMakeFiles/math-test.dir/paddedvector.cpp.o" "CMakeFiles/math-test.dir/vectypes.cpp.o" "CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 81%] Built target math-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: 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-c /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_vector_operations.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 81%] Built target options-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/basic 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 82%] Built target topology-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_math.cpp.o -MF CMakeFiles/simd-test.dir/simd4_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_math.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" 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-DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/report_methods.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" 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'/build/reproducible-path/gromacs-2024.4/build/basic' [ 83%] Built target correlations-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filemd5.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/helpwriting.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 85%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d -o CMakeFiles/fileio-test.dir/filetypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/poscalc.cpp.o -MF CMakeFiles/selection-test.dir/poscalc.cpp.o.d -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/poscalc.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/normalmodes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -MF CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/exactcontinuation.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -MF CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o.d -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/tpitest.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisim.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 86%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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--verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/setbothtime.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 87%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/setstarttime.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -MF CMakeFiles/coordinateio-test.dir/settimestep.cpp.o.d -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/settimestep.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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'/build/reproducible-path/gromacs-2024.4/build/basic' [ 87%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange_equivalence.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" 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-DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 87%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -MF CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd 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../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp [ 87%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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'/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make 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-o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target mdrun-non-integrator-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f 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src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 89%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory 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"CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 90%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make 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"--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 90%] Built target mdrun-coordination-basic-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/interactions.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target selection-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/gmxcalculator.cpp [ 91%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include 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/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include 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-DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target mdrun-simulator-comparison-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbkernelsystem.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 91%] Built target mdrun-coordination-coupling-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests 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/build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/listedtesthelpers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 93%] Built target mdrun-pull-test cd 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/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. 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src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/kernels.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 93%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 94%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/shiftforces.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/filenm.cpp.o -MF CMakeFiles/commandline-test.dir/filenm.cpp.o.d -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/filenm.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 94%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o -MF 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/usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/average.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 95%] Built target commandline-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 97%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 97%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 98%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 98%] Built target nblib-tests cd /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/basic/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/basic/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/basic/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2024.4/build/basic Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -941815889 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.078 0.039 199.7 1: (ns/day) (hour/ns) 1: Performance: 12.945 1.854 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (695 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 2082471626 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 14 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.105 0.052 199.7 1: (ns/day) (hour/ns) 1: Performance: 9.663 2.484 1: [ OK ] GmxApiTest.RunnerBasicMD (693 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -185638922 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.426 0.213 199.9 1: (ns/day) (hour/ns) 1: Performance: 16.648 1.442 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.442 0.221 199.9 1: (ns/day) (hour/ns) 1: Performance: 16.036 1.497 1: [ OK ] GmxApiTest.RunnerReinitialize (1055 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 905419517 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.086 0.043 199.7 1: (ns/day) (hour/ns) 1: Performance: 11.790 2.036 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.102 0.051 199.8 1: (ns/day) (hour/ns) 1: Performance: 9.922 2.419 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (1055 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -269795461 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 27 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.208 0.104 199.9 1: (ns/day) (hour/ns) 1: Performance: 8.104 2.961 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: NOTE: 24 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.105 0.053 199.7 1: (ns/day) (hour/ns) 1: Performance: 6.420 3.739 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (1111 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -416291025 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (925 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (5537 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (5764 ms total) 1: [ PASSED ] 9 tests. 1/87 Test #1: GmxapiExternalInterfaceTests .............. Passed 6.02 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -882181445 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (756 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -692363521 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (652 ms) 2: [----------] 2 tests from GmxApiTest (1409 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (1452 ms total) 2: [ PASSED ] 2 tests. 2/87 Test #2: GmxapiInternalInterfaceTests .............. Passed 1.54 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (20 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (39 ms) 3: [----------] 8 tests from NBlibTest (76 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 3: [----------] 1 test from FourCenter (0 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (6 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (3 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (3 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (3 ms) 3: [----------] 7 tests from ThreeCenter (19 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (3 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (3 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (8 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (3 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (3 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (8 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (39 ms) 3: [----------] 1 test from LinearChainDataFixture (39 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (153 ms total) 3: [ PASSED ] 44 tests. 3/87 Test #3: NbLibListedForcesTests .................... Passed 0.22 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/87 Test #4: NbLibSamplesTestArgon ..................... Passed 0.05 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 5/87 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.10 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (0 ms total) 6: [ PASSED ] 16 tests. 6/87 Test #6: NbLibUtilTests ............................ Passed 0.06 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (12 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (13 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (13 ms total) 7: [ PASSED ] 57 tests. 7/87 Test #7: NbLibSetupTests ........................... Passed 0.10 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (73 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (24 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (19 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (12 ms) 8: [----------] 4 tests from TprReaderTest (130 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (173 ms total) 8: [ PASSED ] 4 tests. 8/87 Test #8: NbLibTprTests ............................. Passed 0.26 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (13 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (7 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (23 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (23 ms total) 9: [ PASSED ] 20 tests. 9/87 Test #9: NbLibIntegrationTests ..................... Passed 0.07 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/87 Test #10: NbLibIntegratorTests ...................... Passed 0.04 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 59 tests from 5 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 11: 11: [----------] 34 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (6 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 34 tests from ReferenceDataTest (8 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 59 tests from 5 test suites ran. (10 ms total) 11: [ PASSED ] 59 tests. 11/87 Test #11: TestUtilsUnitTests ........................ Passed 0.06 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (86 ms) 12: [----------] 1 test from MpiSelfTest (86 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (86 ms total) 12: [ PASSED ] 1 test. 12/87 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.14 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 400 tests from 62 test suites. 13: [----------] Global test environment set-up. 13: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 9 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (30 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (30 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (6 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (3 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (3 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (3 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (1 ms) 13: [----------] 7 tests from TreeValueTransformTest (20 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (5 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (3 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (10 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (2 ms) 13: [----------] 10 tests from TextLineWrapperTest (2 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (3 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (4 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 400 tests from 62 test suites ran. (71 ms total) 13: [ PASSED ] 400 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/87 Test #13: UtilityUnitTests .......................... Passed 0.17 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (38 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (40 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (78 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (78 ms total) 14: [ PASSED ] 2 tests. 14/87 Test #14: UtilityMpiUnitTests ....................... Passed 0.15 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (7 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (4 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (5 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (1 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (4 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (6 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (4 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (3 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (2 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (4 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (6 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (87 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (87 ms total) 15: [ PASSED ] 78 tests. 15/87 Test #15: GmxlibTests ............................... Passed 0.16 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 999 tests from 25 test suites. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [----------] 2 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (3 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (3 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (3 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (11 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (0 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (7 ms) 16: [----------] 2 tests from PrEbinTest (7 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (7 ms) 16: [----------] 1 test from UpdateGroupsCog (7 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 14 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (6 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (4 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (6 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (7 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (35 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (36 ms) 16: [----------] 14 tests from WithParameters/ConstraintsTest (107 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (5 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (21 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (5 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (7 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (8 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (14 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (81 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (5 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (4 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (8 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (22 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (4 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (20 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (19 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (7 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (3 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (7 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (117 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (2 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (6 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (6 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (7 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (5 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (4 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (250 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (5 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (5 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (7 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (7 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (1 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (5 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (7 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (7 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (5 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (7 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (7 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (194 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (5 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (7 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (7 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (7 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (7 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (5 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (7 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (5 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (6 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (4 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (5 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (5 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (5 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (2 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (5 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (187 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (6 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (6 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (3 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (7 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (6 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (4 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (1 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (5 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (7 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (108 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (7 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (6 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (6 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (5 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (5 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (7 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (4 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (1 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (3 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (92 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (6 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (3 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (5 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (4 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (5 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (35 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (5 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (11 ms) 16: [----------] 13 tests from WithParameters/SettleTest (20 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 999 tests from 25 test suites ran. (1224 ms total) 16: [ PASSED ] 999 tests. 16/87 Test #16: MdlibUnitTest ............................. Passed 1.55 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (0 ms) 17: [----------] 1 test from BiasTest (0 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (0 ms) 17: [----------] 1 test from biasGridTest (0 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (200 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (403 ms) 17: [----------] 2 tests from BiasSharingTest (604 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (6 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (3 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (6 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (11 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (7 ms) 17: [----------] 8 tests from WithParameters/BiasTest (38 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (6 ms) 17: [----------] 1 test from WithParameters/UserInputTest (6 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (7 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (19 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (11 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (19 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (71 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (16 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (57 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (75 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (801 ms total) 17: [ PASSED ] 27 tests. 17/87 Test #17: AwhTest ................................... Passed 0.88 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (8 ms) 18: [----------] 2 tests from DensityFittingTest (9 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (9 ms total) 18: [ PASSED ] 18 tests. 18/87 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.08 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (1 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (2 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -1082576453 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (15 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -270869187 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (4 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -9455521 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (12 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -1346963977 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (26 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to 2108633067 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (15 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 19: Setting the LD random seed to -1349534609 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (13 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (89 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (6 ms) 19: [----------] 9 tests from QMMMOptionsTest (7 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (99 ms total) 19: [ PASSED ] 21 tests. 19/87 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.15 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (6 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -167848193 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (10 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (16 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -70650369 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (6 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -536928356 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (14 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to 2147084285 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (3 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to 804126423 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (11 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (36 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -268461061 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (4 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -134219924 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (2 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -16970769 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (69 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 20: Setting the LD random seed to -1111294603 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (64 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (141 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (194 ms total) 20: [ PASSED ] 16 tests. 20/87 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.25 sec test 21 Start 21: AppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/applied_forces/tests 21: Test timeout computed to be: 30 21: [==========] Running 3 tests from 1 test suite. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from ElectricFieldTest 21: [ RUN ] ElectricFieldTest.Static 21: [ OK ] ElectricFieldTest.Static (0 ms) 21: [ RUN ] ElectricFieldTest.Oscillating 21: [ OK ] ElectricFieldTest.Oscillating (0 ms) 21: [ RUN ] ElectricFieldTest.Pulsed 21: [ OK ] ElectricFieldTest.Pulsed (0 ms) 21: [----------] 3 tests from ElectricFieldTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 3 tests from 1 test suite ran. (0 ms total) 21: [ PASSED ] 3 tests. 21/87 Test #21: AppliedForcesUnitTest ..................... Passed 0.03 sec test 22 Start 22: ListedForcesTest 22: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/ListedForcesTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/listed_forces/tests 22: Test timeout computed to be: 30 22: [==========] Running 132 tests from 9 test suites. 22: [----------] Global test environment set-up. 22: [----------] 24 tests from Bond/ListedForcesTest 22: [ RUN ] Bond/ListedForcesTest.Ifunc/0 22: [ OK ] Bond/ListedForcesTest.Ifunc/0 (4 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/1 22: [ OK ] Bond/ListedForcesTest.Ifunc/1 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/2 22: [ OK ] Bond/ListedForcesTest.Ifunc/2 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/3 22: [ OK ] Bond/ListedForcesTest.Ifunc/3 (4 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/4 22: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/5 22: [ OK ] Bond/ListedForcesTest.Ifunc/5 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/6 22: [ OK ] Bond/ListedForcesTest.Ifunc/6 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/7 22: [ OK ] Bond/ListedForcesTest.Ifunc/7 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/8 22: [ OK ] Bond/ListedForcesTest.Ifunc/8 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/9 22: [ OK ] Bond/ListedForcesTest.Ifunc/9 (4 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/10 22: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/11 22: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/12 22: [ OK ] Bond/ListedForcesTest.Ifunc/12 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/13 22: [ OK ] Bond/ListedForcesTest.Ifunc/13 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/14 22: [ OK ] Bond/ListedForcesTest.Ifunc/14 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/15 22: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/16 22: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/17 22: [ OK ] Bond/ListedForcesTest.Ifunc/17 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/18 22: [ OK ] Bond/ListedForcesTest.Ifunc/18 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/19 22: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/20 22: [ OK ] Bond/ListedForcesTest.Ifunc/20 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/21 22: [ OK ] Bond/ListedForcesTest.Ifunc/21 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/22 22: [ OK ] Bond/ListedForcesTest.Ifunc/22 (3 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/23 22: [ OK ] Bond/ListedForcesTest.Ifunc/23 (3 ms) 22: [----------] 24 tests from Bond/ListedForcesTest (72 ms total) 22: 22: [----------] 33 tests from Angle/ListedForcesTest 22: [ RUN ] Angle/ListedForcesTest.Ifunc/0 22: [ OK ] Angle/ListedForcesTest.Ifunc/0 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/1 22: [ OK ] Angle/ListedForcesTest.Ifunc/1 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/2 22: [ OK ] Angle/ListedForcesTest.Ifunc/2 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/3 22: [ OK ] Angle/ListedForcesTest.Ifunc/3 (8 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/4 22: [ OK ] Angle/ListedForcesTest.Ifunc/4 (7 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/5 22: [ OK ] Angle/ListedForcesTest.Ifunc/5 (7 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/6 22: [ OK ] Angle/ListedForcesTest.Ifunc/6 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/7 22: [ OK ] Angle/ListedForcesTest.Ifunc/7 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/8 22: [ OK ] Angle/ListedForcesTest.Ifunc/8 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/9 22: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/10 22: [ OK ] Angle/ListedForcesTest.Ifunc/10 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/11 22: [ OK ] Angle/ListedForcesTest.Ifunc/11 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/12 22: [ OK ] Angle/ListedForcesTest.Ifunc/12 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/13 22: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/14 22: [ OK ] Angle/ListedForcesTest.Ifunc/14 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/15 22: [ OK ] Angle/ListedForcesTest.Ifunc/15 (4 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/16 22: [ OK ] Angle/ListedForcesTest.Ifunc/16 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/17 22: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/18 22: [ OK ] Angle/ListedForcesTest.Ifunc/18 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/19 22: [ OK ] Angle/ListedForcesTest.Ifunc/19 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/20 22: [ OK ] Angle/ListedForcesTest.Ifunc/20 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/21 22: [ OK ] Angle/ListedForcesTest.Ifunc/21 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/22 22: [ OK ] Angle/ListedForcesTest.Ifunc/22 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/23 22: [ OK ] Angle/ListedForcesTest.Ifunc/23 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/24 22: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/25 22: [ OK ] Angle/ListedForcesTest.Ifunc/25 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/26 22: [ OK ] Angle/ListedForcesTest.Ifunc/26 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/27 22: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/28 22: [ OK ] Angle/ListedForcesTest.Ifunc/28 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/29 22: [ OK ] Angle/ListedForcesTest.Ifunc/29 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/30 22: [ OK ] Angle/ListedForcesTest.Ifunc/30 (3 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/31 22: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/32 22: [ OK ] Angle/ListedForcesTest.Ifunc/32 (3 ms) 22: [----------] 33 tests from Angle/ListedForcesTest (119 ms total) 22: 22: [----------] 18 tests from Dihedral/ListedForcesTest 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (7 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (3 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (3 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (3 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (4 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (3 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (3 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (3 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (3 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (3 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (3 ms) 22: [----------] 18 tests from Dihedral/ListedForcesTest (47 ms total) 22: 22: [----------] 12 tests from Polarize/ListedForcesTest 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 22: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 22: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (3 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 22: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (3 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 22: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 22: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 22: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 22: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 22: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 22: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (7 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 22: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (3 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 22: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 22: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (3 ms) 22: [----------] 12 tests from Polarize/ListedForcesTest (23 ms total) 22: 22: [----------] 18 tests from Restraints/ListedForcesTest 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 22: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 22: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 22: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 22: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (7 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 22: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (3 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 22: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (3 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 22: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 22: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (3 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 22: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 22: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (3 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 22: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 22: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 22: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 22: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (3 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 22: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 22: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 22: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (3 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 22: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 22: [----------] 18 tests from Restraints/ListedForcesTest (32 ms total) 22: 22: [----------] 3 tests from BondZeroLength/ListedForcesTest 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (3 ms) 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 22: [----------] 3 tests from BondZeroLength/ListedForcesTest (3 ms total) 22: 22: [----------] 3 tests from AngleZero/ListedForcesTest 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (3 ms) 22: [----------] 3 tests from AngleZero/ListedForcesTest (3 ms total) 22: 22: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (4 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (3 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (3 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (3 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (3 ms) 22: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (19 ms total) 22: 22: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (7 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (3 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 22: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (12 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 132 tests from 9 test suites ran. (352 ms total) 22: [ PASSED ] 132 tests. 22/87 Test #22: ListedForcesTest .......................... Passed 0.42 sec test 23 Start 23: NbnxmTests 23: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/NbnxmTests.xml" 23: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/nbnxm/tests 23: Test timeout computed to be: 30 23: [==========] Running 80 tests from 3 test suites. 23: [----------] Global test environment set-up. 23: [----------] 18 tests from KernelSetupTest 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 23: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 23: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 23: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 23: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 23: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 23: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 23: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 23: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 23: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 23: [----------] 18 tests from KernelSetupTest (0 ms total) 23: 23: [----------] 60 tests from NbnxmKernelTest 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone (20 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch (20 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch (27 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom (27 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone (27 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch (24 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch (27 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom (28 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone (23 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch (24 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch (20 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (27 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom (13 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB (8 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone (1 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch (22 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch (1 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom (15 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom (22 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom (11 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (18 ms) 23: [----------] 60 tests from NbnxmKernelTest (643 ms total) 23: 23: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 23: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 23: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 23: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 23: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 23: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 80 tests from 3 test suites ran. (644 ms total) 23: [ PASSED ] 80 tests. 23/87 Test #23: NbnxmTests ................................ Passed 0.76 sec test 24 Start 24: CommandLineUnitTests 24: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests 24: Test timeout computed to be: 30 24: [==========] Running 60 tests from 7 test suites. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from CommandLineHelpModuleTest 24: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 24: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (13 ms) 24: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 24: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 24: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 24: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 24: [----------] 3 tests from CommandLineHelpModuleTest (14 ms total) 24: 24: [----------] 7 tests from CommandLineHelpWriterTest 24: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 24: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 24: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 24: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 24: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 24: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 24: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 24: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 24: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 24: 24: [----------] 6 tests from CommandLineModuleManagerTest 24: [ RUN ] CommandLineModuleManagerTest.RunsModule 24: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 24: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 24: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 24: 24: [----------] 13 tests from CommandLineParserTest 24: [ RUN ] CommandLineParserTest.HandlesSingleValues 24: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 24: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 24: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 24: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 24: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 24: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesString 24: [ OK ] CommandLineParserTest.HandlesString (0 ms) 24: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 24: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 24: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 24: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 24: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 24: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 24: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 24: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 24: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 24: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 24: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 24: [----------] 13 tests from CommandLineParserTest (0 ms total) 24: 24: [----------] 6 tests from CommandLineProgramContextTest 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 24: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 24: 24: [----------] 3 tests from OutputNamesTest 24: [ RUN ] OutputNamesTest.CanBeSuffixed 24: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 24: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 24: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 24: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 24: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 24: [----------] 3 tests from OutputNamesTest (0 ms total) 24: 24: [----------] 22 tests from ParseCommonArgsTest 24: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 24: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 24: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 24: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 24: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 24: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 24: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 24: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 24: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 24: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 24: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 24: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 24: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 24: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 24: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 24: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 24: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 24: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 24: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 24: Value is /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 24: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 24: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 24: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 24: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 24: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 24: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 24: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 24: [----------] 22 tests from ParseCommonArgsTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 60 tests from 7 test suites ran. (16 ms total) 24: [ PASSED ] 60 tests. 24/87 Test #24: CommandLineUnitTests ...................... Passed 0.08 sec test 25 Start 25: DomDecTests 25: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/DomDecTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests 25: Test timeout computed to be: 30 25: [==========] Running 9 tests from 2 test suites. 25: [----------] Global test environment set-up. 25: [----------] 7 tests from HashedMap 25: [ RUN ] HashedMap.InsertsFinds 25: [ OK ] HashedMap.InsertsFinds (0 ms) 25: [ RUN ] HashedMap.NegativeKeysWork 25: [ OK ] HashedMap.NegativeKeysWork (0 ms) 25: [ RUN ] HashedMap.InsertsErases 25: [ OK ] HashedMap.InsertsErases (0 ms) 25: [ RUN ] HashedMap.InsertsOrAssigns 25: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 25: [ RUN ] HashedMap.Clears 25: [ OK ] HashedMap.Clears (0 ms) 25: [ RUN ] HashedMap.LinkedEntries 25: [ OK ] HashedMap.LinkedEntries (0 ms) 25: [ RUN ] HashedMap.ResizesTable 25: [ OK ] HashedMap.ResizesTable (0 ms) 25: [----------] 7 tests from HashedMap (0 ms total) 25: 25: [----------] 2 tests from LocalAtomSetManager 25: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 25: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 25: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 25: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 25: [----------] 2 tests from LocalAtomSetManager (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 9 tests from 2 test suites ran. (0 ms total) 25: [ PASSED ] 9 tests. 25/87 Test #25: DomDecTests ............................... Passed 0.08 sec test 26 Start 26: DomDecMpiTests 26: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/DomDecMpiTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/domdec/tests 26: Test timeout computed to be: 30 26: [==========] Running 4 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 4 tests from HaloExchangeTest 26: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 26: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (83 ms) 26: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 26: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (72 ms) 26: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 26: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (67 ms) 26: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 26: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (103 ms) 26: [----------] 4 tests from HaloExchangeTest (327 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 4 tests from 1 test suite ran. (327 ms total) 26: [ PASSED ] 4 tests. 26/87 Test #26: DomDecMpiTests ............................ Passed 0.41 sec test 27 Start 27: EwaldUnitTests 27: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/EwaldUnitTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/ewald/tests 27: Test timeout computed to be: 30 27: [==========] Running 407 tests from 9 test suites. 27: [----------] Global test environment set-up. 27: [----------] 6 tests from SeparatePmeRanksPermittedTest 27: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 27: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 27: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 27: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 27: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 27: 27: [----------] 108 tests from Pme_SplineAndSpreadTest 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (124 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (23 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (30 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (8 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (23 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (3 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (23 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (10 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (10 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (15 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (10 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (6 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (11 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (14 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (8 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (19 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (5 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (13 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (13 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (10 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (9 ms) 27: [----------] 108 tests from Pme_SplineAndSpreadTest (553 ms total) 27: 27: [----------] 64 tests from Pme_SolveTest 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (14 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (1 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (18 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (7 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (7 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [----------] 64 tests from Pme_SolveTest (63 ms total) 27: 27: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (2 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (11 ms total) 27: 27: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (7 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (6 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (1 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (20 ms total) 27: 27: [----------] 64 tests from PmeDiffEps_SolveTest 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (9 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (2 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (6 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [----------] 64 tests from PmeDiffEps_SolveTest (24 ms total) 27: 27: [----------] 72 tests from Pme_GatherTest 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (2 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (7 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (1 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (1 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (4 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (1 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [----------] 72 tests from Pme_GatherTest (30 ms total) 27: 27: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 27: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 27: 27: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (9 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (5 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (10 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (8 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (3 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (8 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 27: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (63 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 407 tests from 9 test suites ran. (788 ms total) 27: [ PASSED ] 311 tests. 27: [ SKIPPED ] 96 tests, listed below: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27/87 Test #27: EwaldUnitTests ............................ Passed 0.89 sec test 28 Start 28: FFTUnitTests 28: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/FFTUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fft/tests 28: Test timeout computed to be: 1920 28: [==========] Running 15 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 2 tests from ManyFFTTest 28: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 28: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (13 ms) 28: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 28: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (9 ms) 28: [----------] 2 tests from ManyFFTTest (22 ms total) 28: 28: [----------] 1 test from FFTTest 28: [ RUN ] FFTTest.Real2DLength18_15Test 28: [ OK ] FFTTest.Real2DLength18_15Test (1 ms) 28: [----------] 1 test from FFTTest (1 ms total) 28: 28: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (6 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (1 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (2 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (11 ms) 28: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (24 ms total) 28: 28: [----------] 2 tests from Works/ParameterizedFFTTest3D 28: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 28: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 28: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 28: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 28: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 15 tests from 4 test suites ran. (50 ms total) 28: [ PASSED ] 15 tests. 28/87 Test #28: FFTUnitTests .............................. Passed 0.16 sec test 29 Start 29: GpuUtilsUnitTests 29: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gpu_utils/tests 29: Test timeout computed to be: 30 29: [==========] Running 64 tests from 22 test suites. 29: [----------] Global test environment set-up. 29: [----------] 2 tests from ClfftInitializer 29: [ RUN ] ClfftInitializer.SingleInitializationWorks 29: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 29: [ RUN ] ClfftInitializer.TwoInitializationsWork 29: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 29: [----------] 2 tests from ClfftInitializer (0 ms total) 29: 29: [----------] 1 test from DevicesAvailable 29: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 29: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 29: [----------] 1 test from DevicesAvailable (0 ms total) 29: 29: [----------] 1 test from DeviceStreamManagerTest 29: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 29: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 29: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 29: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 29: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 29: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 29: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 29: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.Swap 29: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.Comparison 29: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 29: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 29: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.Swap 29: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.Comparison 29: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 29: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.Swap 29: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.Comparison 29: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 29: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 29: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.Swap 29: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.Comparison 29: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 29: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 29: 29: [----------] 1 test from HostAllocatorUntypedTest 29: [ RUN ] HostAllocatorUntypedTest.Comparison 29: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 29: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.Move 29: [ OK ] AllocatorTest/0.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/0 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.Move 29: [ OK ] AllocatorTest/1.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/1 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 29: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.Move 29: [ OK ] AllocatorTest/2.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/2 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.Move 29: [ OK ] AllocatorTest/3.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/3 (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 64 tests from 22 test suites ran. (0 ms total) 29: [ PASSED ] 64 tests. 29/87 Test #29: GpuUtilsUnitTests ......................... Passed 0.06 sec test 30 Start 30: HardwareUnitTests 30: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/HardwareUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/hardware/tests 30: Test timeout computed to be: 30 30: [==========] Running 21 tests from 9 test suites. 30: [----------] Global test environment set-up. 30: [----------] 1 test from CpuInfoTest 30: [ RUN ] CpuInfoTest.SupportLevel 30: [ OK ] CpuInfoTest.SupportLevel (0 ms) 30: [----------] 1 test from CpuInfoTest (0 ms total) 30: 30: [----------] 4 tests from HardwareTopologyTest 30: [ RUN ] HardwareTopologyTest.Execute 30: [ OK ] HardwareTopologyTest.Execute (15 ms) 30: [ RUN ] HardwareTopologyTest.HwlocExecute 30: [ OK ] HardwareTopologyTest.HwlocExecute (18 ms) 30: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 30: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (11 ms) 30: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 30: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (17 ms) 30: [----------] 4 tests from HardwareTopologyTest (62 ms total) 30: 30: [----------] 1 test from DevicesManagerTest 30: [ RUN ] DevicesManagerTest.Serialization 30: [ OK ] DevicesManagerTest.Serialization (0 ms) 30: [----------] 1 test from DevicesManagerTest (0 ms total) 30: 30: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (19 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (1 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (6 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 30: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (28 ms total) 30: 30: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (7 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (2 ms) 30: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (11 ms total) 30: 30: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 30: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (3 ms) 30: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 30: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (4 ms total) 30: 30: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 30: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (28 ms) 30: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (28 ms total) 30: 30: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 30: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (100 ms) 30: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (100 ms total) 30: 30: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 30: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (133 ms) 30: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (134 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 21 tests from 9 test suites ran. (370 ms total) 30: [ PASSED ] 21 tests. 30/87 Test #30: HardwareUnitTests ......................... Passed 0.41 sec test 31 Start 31: MathUnitTests 31: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MathUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/math/tests 31: Test timeout computed to be: 30 31: [==========] Running 304 tests from 38 test suites. 31: [----------] Global test environment set-up. 31: [----------] 1 test from EmptyArrayRefWithPaddingTest 31: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 31: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 31: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 31: 31: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 31: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 31: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 31: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 31: 31: [----------] 2 tests from InvertBoxMatrixTest 31: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 31: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 31: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 31: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 31: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 31: 31: [----------] 11 tests from TranslateAndScaleTest 31: [ RUN ] TranslateAndScaleTest.identityTransformation 31: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 31: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 31: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 31: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 31: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingIdentity 31: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 31: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 31: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 31: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 31: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 31: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 31: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 31: 31: [----------] 3 tests from AffineTransformationTest 31: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 31: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 31: [ RUN ] AffineTransformationTest.applyTransformationToVectors 31: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 31: [ RUN ] AffineTransformationTest.retrieveGradient 31: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 31: [----------] 3 tests from AffineTransformationTest (0 ms total) 31: 31: [----------] 14 tests from DensitySimilarityTest 31: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 31: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 31: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 31: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 31: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 31: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 31: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 31: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 31: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 31: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 31: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 31: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (39 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 31: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (32 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 31: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 31: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (6 ms) 31: [ RUN ] DensitySimilarityTest.NormalizationCorrect 31: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 31: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 31: [----------] 14 tests from DensitySimilarityTest (79 ms total) 31: 31: [----------] 6 tests from StructureSimilarityTest 31: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 31: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 31: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 31: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 31: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 31: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 31: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 31: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 31: [----------] 6 tests from StructureSimilarityTest (0 ms total) 31: 31: [----------] 8 tests from ExponentialMovingAverage 31: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 31: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 31: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 31: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 31: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 31: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 31: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 31: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 31: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 31: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 31: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 31: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 31: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 31: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 31: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 31: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 31: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 31: 31: [----------] 21 tests from FunctionTest 31: [ RUN ] FunctionTest.StaticLog2 31: [ OK ] FunctionTest.StaticLog2 (0 ms) 31: [ RUN ] FunctionTest.Log2I32Bit 31: [ OK ] FunctionTest.Log2I32Bit (0 ms) 31: [ RUN ] FunctionTest.Log2I64Bit 31: [ OK ] FunctionTest.Log2I64Bit (0 ms) 31: [ RUN ] FunctionTest.GreatestCommonDivisor 31: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 31: [ RUN ] FunctionTest.InvsqrtFloat 31: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 31: [ RUN ] FunctionTest.InvsqrtDouble 31: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 31: [ RUN ] FunctionTest.InvsqrtInteger 31: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 31: [ RUN ] FunctionTest.InvcbrtFloat 31: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 31: [ RUN ] FunctionTest.InvcbrtDouble 31: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 31: [ RUN ] FunctionTest.InvcbrtInteger 31: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 31: [ RUN ] FunctionTest.SixthrootFloat 31: [ OK ] FunctionTest.SixthrootFloat (0 ms) 31: [ RUN ] FunctionTest.SixthrootDouble 31: [ OK ] FunctionTest.SixthrootDouble (1 ms) 31: [ RUN ] FunctionTest.SixthrootInteger 31: [ OK ] FunctionTest.SixthrootInteger (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootFloat 31: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootDouble 31: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootInteger 31: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 31: [ RUN ] FunctionTest.Powers 31: [ OK ] FunctionTest.Powers (0 ms) 31: [ RUN ] FunctionTest.ErfInvFloat 31: [ OK ] FunctionTest.ErfInvFloat (0 ms) 31: [ RUN ] FunctionTest.ErfInvDouble 31: [ OK ] FunctionTest.ErfInvDouble (0 ms) 31: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 31: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 31: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 31: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 31: [----------] 21 tests from FunctionTest (2 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 31: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 31: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 31: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 31: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 31: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 31: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 31: 31: [----------] 4 tests from GaussianOn1DLattice 31: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 31: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 31: [ RUN ] GaussianOn1DLattice.isCorrect 31: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 31: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 31: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 31: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 31: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 31: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 31: 31: [----------] 9 tests from GaussTransformTest 31: [ RUN ] GaussTransformTest.isZeroUponConstruction 31: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 31: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 31: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 31: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 31: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 31: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 31: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 31: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 31: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 31: [ RUN ] GaussTransformTest.view 31: [ OK ] GaussTransformTest.view (0 ms) 31: [----------] 9 tests from GaussTransformTest (0 ms total) 31: 31: [----------] 3 tests from DensityFittingForce 31: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 31: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 31: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 31: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 31: [ RUN ] DensityFittingForce.pullsTowardsDerivative 31: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 31: [----------] 3 tests from DensityFittingForce (0 ms total) 31: 31: [----------] 2 tests from InvertMatrixTest 31: [ RUN ] InvertMatrixTest.IdentityIsImpotent 31: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 31: [ RUN ] InvertMatrixTest.ComputesInverse 31: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 31: [----------] 2 tests from InvertMatrixTest (0 ms total) 31: 31: [----------] 17 tests from MatrixTest 31: [ RUN ] MatrixTest.canSetFromArray 31: [ OK ] MatrixTest.canSetFromArray (0 ms) 31: [ RUN ] MatrixTest.canSetStaticallyFromList 31: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 31: [ RUN ] MatrixTest.canConstructAndFill 31: [ OK ] MatrixTest.canConstructAndFill (0 ms) 31: [ RUN ] MatrixTest.canSetValues 31: [ OK ] MatrixTest.canSetValues (0 ms) 31: [ RUN ] MatrixTest.canCopyAssign 31: [ OK ] MatrixTest.canCopyAssign (0 ms) 31: [ RUN ] MatrixTest.canSwap 31: [ OK ] MatrixTest.canSwap (0 ms) 31: [ RUN ] MatrixTest.staticMultiDimArrayExtent 31: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 31: [ RUN ] MatrixTest.determinantWorks 31: [ OK ] MatrixTest.determinantWorks (0 ms) 31: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 31: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 31: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 31: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 31: [ RUN ] MatrixTest.traceWorks 31: [ OK ] MatrixTest.traceWorks (0 ms) 31: [ RUN ] MatrixTest.transposeWorks 31: [ OK ] MatrixTest.transposeWorks (0 ms) 31: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 31: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 31: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 31: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 31: [ RUN ] MatrixTest.canFillLegacyMatrix 31: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 31: [ RUN ] MatrixTest.IdentityMatrix 31: [ OK ] MatrixTest.IdentityMatrix (0 ms) 31: [ RUN ] MatrixTest.MatrixVectorMultiplication 31: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 31: [----------] 17 tests from MatrixTest (0 ms total) 31: 31: [----------] 25 tests from MultiDimArrayTest 31: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 31: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 31: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 31: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 31: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 31: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 31: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 31: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 31: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 31: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 31: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 31: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 31: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSwapStatic 31: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSwapDynamic 31: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 31: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 31: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 31: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 31: [ RUN ] MultiDimArrayTest.conversionToView 31: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 31: [ RUN ] MultiDimArrayTest.conversionToConstView 31: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 31: [ RUN ] MultiDimArrayTest.viewBegin 31: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 31: [ RUN ] MultiDimArrayTest.viewEnd 31: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 31: [ RUN ] MultiDimArrayTest.constViewConstBegin 31: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 31: [ RUN ] MultiDimArrayTest.constViewConstEnd 31: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 31: [----------] 25 tests from MultiDimArrayTest (0 ms total) 31: 31: [----------] 4 tests from MultiDimArrayToMdSpanTest 31: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 31: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 31: 31: [----------] 9 tests from NelderMeadSimplexTest 31: [ RUN ] NelderMeadSimplexTest.BestVertex 31: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 31: [ RUN ] NelderMeadSimplexTest.WorstVertex 31: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 31: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 31: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 31: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 31: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 31: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 31: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 31: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 31: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 31: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 31: [ RUN ] NelderMeadSimplexTest.OrientedLength 31: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 31: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 31: 31: [----------] 2 tests from NelderMead 31: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 31: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (23 ms) 31: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 31: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 31: [----------] 2 tests from NelderMead (23 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ResizeWorks 31: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ReserveWorks 31: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanCopyAssign 31: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanMoveAssign 31: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanSwap 31: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ResizeWorks 31: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ReserveWorks 31: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanCopyAssign 31: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanMoveAssign 31: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanSwap 31: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ResizeWorks 31: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ReserveWorks 31: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanCopyAssign 31: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanMoveAssign 31: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanSwap 31: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 31: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ResizeWorks 31: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ReserveWorks 31: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanCopyAssign 31: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanMoveAssign 31: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanSwap 31: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 31: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ResizeWorks 31: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ReserveWorks 31: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanCopyAssign 31: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanMoveAssign 31: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanSwap 31: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ResizeWorks 31: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ReserveWorks 31: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanCopyAssign 31: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanMoveAssign 31: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanSwap 31: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ResizeWorks 31: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ReserveWorks 31: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanCopyAssign 31: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanMoveAssign 31: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanSwap 31: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ResizeWorks 31: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ReserveWorks 31: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanCopyAssign 31: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanMoveAssign 31: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanSwap 31: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 31: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ResizeWorks 31: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ReserveWorks 31: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanCopyAssign 31: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanMoveAssign 31: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanSwap 31: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 31: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ResizeWorks 31: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ReserveWorks 31: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanCopyAssign 31: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanMoveAssign 31: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanSwap 31: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 31: 31: [----------] 40 tests from RVecTest 31: [ RUN ] RVecTest.CanBeStoredInVector 31: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 31: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 31: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 31: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 31: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 31: [ RUN ] RVecTest.WorksAsMutable_rvec 31: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 31: [ RUN ] RVecTest.WorksAs_rvec_Array 31: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 31: [ RUN ] RVecTest.ComparesEqual 31: [ OK ] RVecTest.ComparesEqual (0 ms) 31: [ RUN ] RVecTest.ComparesUnequal 31: [ OK ] RVecTest.ComparesUnequal (0 ms) 31: [ RUN ] RVecTest.CanAddRVecToRvec 31: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 31: [ RUN ] RVecTest.CanAddAssignRVecToRvec 31: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 31: [ RUN ] RVecTest.CanSubtractRVecFromRvec 31: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 31: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 31: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 31: [ RUN ] RVecTest.CanDotProductRVecByRvec 31: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 31: [ RUN ] RVecTest.CanCrossProductRVecByRvec 31: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 31: [ RUN ] RVecTest.CanDivideRVecInplace 31: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 31: [ RUN ] RVecTest.CanScaleRVec 31: [ OK ] RVecTest.CanScaleRVec (0 ms) 31: [ RUN ] RVecTest.CanDivideRVec 31: [ OK ] RVecTest.CanDivideRVec (0 ms) 31: [ RUN ] RVecTest.CanDoUnitvFromRVec 31: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 31: [ RUN ] RVecTest.CanSqLengthOfRVec 31: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanLengthOfRVec 31: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanCastToRVec 31: [ OK ] RVecTest.CanCastToRVec (0 ms) 31: [ RUN ] RVecTest.CanCastToDVec 31: [ OK ] RVecTest.CanCastToDVec (0 ms) 31: [ RUN ] RVecTest.CanLeftScalarMultiply 31: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 31: [ RUN ] RVecTest.CanRightScalarMultiply 31: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 31: [ RUN ] RVecTest.CanGetUnitvFromRVec 31: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 31: [ RUN ] RVecTest.CanGetSqLengthOfRVec 31: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanGetLengthOfRVec 31: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanDoCrossProductOfRVec 31: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 31: [ RUN ] RVecTest.CanDoDotProductOfRVec 31: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 31: [ RUN ] RVecTest.CanScaleByVector 31: [ OK ] RVecTest.CanScaleByVector (0 ms) 31: [ RUN ] RVecTest.CanNegate 31: [ OK ] RVecTest.CanNegate (0 ms) 31: [ RUN ] RVecTest.asIVec 31: [ OK ] RVecTest.asIVec (0 ms) 31: [ RUN ] RVecTest.elementWiseMin 31: [ OK ] RVecTest.elementWiseMin (0 ms) 31: [ RUN ] RVecTest.elementWiseMax 31: [ OK ] RVecTest.elementWiseMax (0 ms) 31: [ RUN ] RVecTest.WorksAs_dvec_Reference 31: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 31: [ RUN ] RVecTest.WorksAs_ivec_Reference 31: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 31: [ RUN ] RVecTest.WorksAs_rvec_Reference 31: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 31: [ RUN ] RVecTest.CopyConstructorWorks 31: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 31: [ RUN ] RVecTest.CopyAssignmentWorks 31: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 31: [ RUN ] RVecTest.MoveConstructorWorks 31: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 31: [ RUN ] RVecTest.MoveAssignmentWorks 31: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 31: [----------] 40 tests from RVecTest (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 304 tests from 38 test suites ran. (106 ms total) 31: [ PASSED ] 304 tests. 31/87 Test #31: MathUnitTests ............................. Passed 0.16 sec test 32 Start 32: MdrunUtilityUnitTests 32: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests 32: Test timeout computed to be: 30 32: [==========] Running 21 tests from 2 test suites. 32: [----------] Global test environment set-up. 32: [----------] 4 tests from MDModulesNotifierTest 32: [ RUN ] MDModulesNotifierTest.AddConsumer 32: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 32: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 32: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 32: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 32: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 32: 32: [----------] 17 tests from ThreadAffinityTest 32: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 32: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 32: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (4 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 32: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 32: NOTE: Affinity setting failed. 32: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 32: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (23 ms) 32: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 32: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 32: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 32: NOTE: Affinity setting for 1/2 threads failed. 32: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 32: [----------] 17 tests from ThreadAffinityTest (30 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 21 tests from 2 test suites ran. (30 ms total) 32: [ PASSED ] 21 tests. 32/87 Test #32: MdrunUtilityUnitTests ..................... Passed 0.06 sec test 33 Start 33: MdrunUtilityMpiUnitTests 33: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdrunutility/tests 33: Test timeout computed to be: 30 33: [==========] Running 13 tests from 2 test suites. 33: [----------] Global test environment set-up. 33: [----------] 6 tests from ThreadAffinityMultiRankTest 33: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 33: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (278 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 33: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (244 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 33: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (180 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 33: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (115 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 33: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (200 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 33: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (139 ms) 33: [----------] 6 tests from ThreadAffinityMultiRankTest (1158 ms total) 33: 33: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (211 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (203 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (143 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (182 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (141 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (131 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (167 ms) 33: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (1183 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 13 tests from 2 test suites ran. (2342 ms total) 33: [ PASSED ] 13 tests. 33/87 Test #33: MdrunUtilityMpiUnitTests .................. Passed 2.37 sec test 34 Start 34: MDSpanTests 34: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MDSpanTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdspan/tests 34: Test timeout computed to be: 30 34: [==========] Running 32 tests from 7 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from BasicAccessorPolicy 34: [ RUN ] BasicAccessorPolicy.Decay 34: [ OK ] BasicAccessorPolicy.Decay (0 ms) 34: [ RUN ] BasicAccessorPolicy.Access 34: [ OK ] BasicAccessorPolicy.Access (0 ms) 34: [ RUN ] BasicAccessorPolicy.Offset 34: [ OK ] BasicAccessorPolicy.Offset (0 ms) 34: [ RUN ] BasicAccessorPolicy.CopyAccessor 34: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 34: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 34: 34: [----------] 4 tests from ExtentsTest 34: [ RUN ] ExtentsTest.Construction 34: [ OK ] ExtentsTest.Construction (0 ms) 34: [ RUN ] ExtentsTest.PurelyStatic 34: [ OK ] ExtentsTest.PurelyStatic (0 ms) 34: [ RUN ] ExtentsTest.RankNought 34: [ OK ] ExtentsTest.RankNought (0 ms) 34: [ RUN ] ExtentsTest.Assignment 34: [ OK ] ExtentsTest.Assignment (0 ms) 34: [----------] 4 tests from ExtentsTest (0 ms total) 34: 34: [----------] 8 tests from MdSpanExtension 34: [ RUN ] MdSpanExtension.SlicingAllStatic 34: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 34: [ RUN ] MdSpanExtension.SlicingDynamic 34: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 34: [ RUN ] MdSpanExtension.SlicingAllStatic3D 34: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 34: [ RUN ] MdSpanExtension.SlicingEqualsView3D 34: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 34: [ RUN ] MdSpanExtension.additionWorks 34: [ OK ] MdSpanExtension.additionWorks (0 ms) 34: [ RUN ] MdSpanExtension.subtractionWorks 34: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 34: [ RUN ] MdSpanExtension.multiplicationWorks 34: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 34: [ RUN ] MdSpanExtension.divisionWorks 34: [ OK ] MdSpanExtension.divisionWorks (0 ms) 34: [----------] 8 tests from MdSpanExtension (0 ms total) 34: 34: [----------] 3 tests from LayoutTests 34: [ RUN ] LayoutTests.LayoutRightConstruction 34: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 34: [ RUN ] LayoutTests.LayoutRightProperties 34: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 34: [ RUN ] LayoutTests.LayoutRightOperator 34: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 34: [----------] 3 tests from LayoutTests (0 ms total) 34: 34: [----------] 1 test from MdSpanTest 34: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 34: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 34: [----------] 1 test from MdSpanTest (0 ms total) 34: 34: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 34: [ RUN ] MdSpanTest/0.Rank 34: [ OK ] MdSpanTest/0.Rank (0 ms) 34: [ RUN ] MdSpanTest/0.DynamicRank 34: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 34: [ RUN ] MdSpanTest/0.Extents 34: [ OK ] MdSpanTest/0.Extents (0 ms) 34: [ RUN ] MdSpanTest/0.Strides 34: [ OK ] MdSpanTest/0.Strides (0 ms) 34: [ RUN ] MdSpanTest/0.Properties 34: [ OK ] MdSpanTest/0.Properties (0 ms) 34: [ RUN ] MdSpanTest/0.Operator 34: [ OK ] MdSpanTest/0.Operator (0 ms) 34: [----------] 6 tests from MdSpanTest/0 (0 ms total) 34: 34: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 34: [ RUN ] MdSpanTest/1.Rank 34: [ OK ] MdSpanTest/1.Rank (0 ms) 34: [ RUN ] MdSpanTest/1.DynamicRank 34: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 34: [ RUN ] MdSpanTest/1.Extents 34: [ OK ] MdSpanTest/1.Extents (0 ms) 34: [ RUN ] MdSpanTest/1.Strides 34: [ OK ] MdSpanTest/1.Strides (0 ms) 34: [ RUN ] MdSpanTest/1.Properties 34: [ OK ] MdSpanTest/1.Properties (0 ms) 34: [ RUN ] MdSpanTest/1.Operator 34: [ OK ] MdSpanTest/1.Operator (0 ms) 34: [----------] 6 tests from MdSpanTest/1 (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 32 tests from 7 test suites ran. (0 ms total) 34: [ PASSED ] 32 tests. 34/87 Test #34: MDSpanTests ............................... Passed 0.04 sec test 35 Start 35: MdtypesUnitTest 35: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdtypesUnitTest.xml" 35: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/mdtypes/tests 35: Test timeout computed to be: 30 35: [==========] Running 97 tests from 7 test suites. 35: [----------] Global test environment set-up. 35: [----------] 4 tests from ForeingLambdaTermsDhdl 35: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 35: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 35: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 35: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 35: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 35: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 35: 35: [----------] 4 tests from ObservablesReducerTest 35: [ RUN ] ObservablesReducerTest.CanMoveAssign 35: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 35: [ RUN ] ObservablesReducerTest.CanMoveConstruct 35: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 35: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 35: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 35: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 35: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 35: [----------] 4 tests from ObservablesReducerTest (0 ms total) 35: 35: [----------] 2 tests from CheckpointDataTest 35: [ RUN ] CheckpointDataTest.SingleDataTest 35: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 35: [ RUN ] CheckpointDataTest.MultiDataTest 35: [ OK ] CheckpointDataTest.MultiDataTest (6 ms) 35: [----------] 2 tests from CheckpointDataTest (7 ms total) 35: 35: [----------] 7 tests from ForceBuffers 35: [ RUN ] ForceBuffers.ConstructsUnpinned 35: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 35: [ RUN ] ForceBuffers.ConstructsPinned 35: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 35: [ RUN ] ForceBuffers.ConstructsEmpty 35: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 35: [ RUN ] ForceBuffers.ResizeWorks 35: [ OK ] ForceBuffers.ResizeWorks (0 ms) 35: [ RUN ] ForceBuffers.PaddingWorks 35: [ OK ] ForceBuffers.PaddingWorks (0 ms) 35: [ RUN ] ForceBuffers.CopyWorks 35: [ OK ] ForceBuffers.CopyWorks (0 ms) 35: [ RUN ] ForceBuffers.CopyDoesNotPin 35: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 35: [----------] 7 tests from ForceBuffers (0 ms total) 35: 35: [----------] 5 tests from MultipleTimeStepping 35: [ RUN ] MultipleTimeStepping.ChecksNumLevels 35: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 35: [ RUN ] MultipleTimeStepping.SelectsForceGroups 35: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksStepFactor 35: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 35: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksIntegrator 35: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 35: [----------] 5 tests from MultipleTimeStepping (0 ms total) 35: 35: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 35: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 35: 35: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 35: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 97 tests from 7 test suites ran. (8 ms total) 35: [ PASSED ] 97 tests. 35/87 Test #35: MdtypesUnitTest ........................... Passed 0.05 sec test 36 Start 36: OnlineHelpUnitTests 36: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/onlinehelp/tests 36: Test timeout computed to be: 30 36: [==========] Running 22 tests from 4 test suites. 36: [----------] Global test environment set-up. 36: [----------] 6 tests from TextTableFormatterTest 36: [ RUN ] TextTableFormatterTest.HandlesBasicCase 36: [ OK ] TextTableFormatterTest.HandlesBasicCase (2 ms) 36: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 36: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesIndentation 36: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms) 36: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 36: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (6 ms) 36: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 36: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (3 ms) 36: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 36: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 36: [----------] 6 tests from TextTableFormatterTest (14 ms total) 36: 36: [----------] 3 tests from HelpManagerTest 36: [ RUN ] HelpManagerTest.HandlesRootTopic 36: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 36: [ RUN ] HelpManagerTest.HandlesSubTopics 36: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 36: [ RUN ] HelpManagerTest.HandlesInvalidTopics 36: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 36: [----------] 3 tests from HelpManagerTest (0 ms total) 36: 36: [----------] 2 tests from HelpTopicFormattingTest 36: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 36: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (7 ms) 36: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 36: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 36: [----------] 2 tests from HelpTopicFormattingTest (7 ms total) 36: 36: [----------] 11 tests from HelpWriterContextTest 36: [ RUN ] HelpWriterContextTest.FormatsParagraphs 36: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 36: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 36: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 36: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralText 36: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 36: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 36: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsBulletList 36: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 36: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 36: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsGridTable 36: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsTitles 36: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 36: [----------] 11 tests from HelpWriterContextTest (1 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 22 tests from 4 test suites ran. (24 ms total) 36: [ PASSED ] 22 tests. 36/87 Test #36: OnlineHelpUnitTests ....................... Passed 0.05 sec test 37 Start 37: OptionsUnitTests 37: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/OptionsUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/options/tests 37: Test timeout computed to be: 30 37: [==========] Running 111 tests from 18 test suites. 37: [----------] Global test environment set-up. 37: [----------] 5 tests from AbstractOptionStorageTest 37: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 37: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 37: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 37: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 37: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 37: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 37: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 37: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 37: 37: [----------] 10 tests from FileNameOptionTest 37: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 37: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 37: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 37: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 37: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 37: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 37: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 37: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 37: [----------] 10 tests from FileNameOptionTest (0 ms total) 37: 37: [----------] 15 tests from FileNameOptionManagerTest 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 37: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 37: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 37: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 37: 37: [----------] 1 test from OptionsTest 37: [ RUN ] OptionsTest.FailsOnNonsafeStorage 37: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 37: [----------] 1 test from OptionsTest (0 ms total) 37: 37: [----------] 9 tests from OptionsAssignerTest 37: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 37: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 37: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 37: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 37: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMissingValue 37: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesExtraValue 37: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesGroups 37: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesSections 37: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 37: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 37: [----------] 9 tests from OptionsAssignerTest (0 ms total) 37: 37: [----------] 4 tests from OptionsAssignerBooleanTest 37: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 37: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 37: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 37: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 37: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 37: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 37: 37: [----------] 13 tests from OptionsAssignerIntegerTest 37: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 37: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 37: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 37: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 37: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 37: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 37: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 37: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 37: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 37: 37: [----------] 5 tests from OptionsAssignerDoubleTest 37: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 37: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 37: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 37: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 37: 37: [----------] 9 tests from OptionsAssignerStringTest 37: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 37: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 37: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 37: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 37: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 37: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 37: 37: [----------] 6 tests from OptionsAssignerEnumTest 37: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 37: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 37: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 37: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 37: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 37: 37: [----------] 8 tests from RepeatingOptionSectionTest 37: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 37: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 37: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 37: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 37: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 37: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 37: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 37: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 37: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 37: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 37: 37: [----------] 1 test from TimeUnitManagerTest 37: [ RUN ] TimeUnitManagerTest.BasicOperations 37: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 37: [----------] 1 test from TimeUnitManagerTest (0 ms total) 37: 37: [----------] 4 tests from TimeUnitBehaviorTest 37: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 37: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 37: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 37: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 37: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 37: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 37: 37: [----------] 2 tests from TreeValueSupportAssignTest 37: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 37: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 37: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 37: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 37: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 37: 37: [----------] 1 test from TreeValueSupportAssignErrorTest 37: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 37: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 37: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 37: 37: [----------] 5 tests from TreeValueSupportCheckTest 37: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 37: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 37: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 37: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 37: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 37: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 37: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 37: 37: [----------] 6 tests from TreeValueSupportAdjustTest 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (6 ms) 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (3 ms) 37: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 37: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 37: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 37: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 37: [----------] 6 tests from TreeValueSupportAdjustTest (10 ms total) 37: 37: [----------] 7 tests from TreeValueSupportTest 37: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 37: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 37: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsInt64Option 37: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsStringOption 37: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsFloatOption 37: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 37: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsEnumOption 37: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 37: [----------] 7 tests from TreeValueSupportTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 111 tests from 18 test suites ran. (17 ms total) 37: [ PASSED ] 111 tests. 37/87 Test #37: OptionsUnitTests .......................... Passed 0.04 sec test 38 Start 38: PbcutilUnitTest 38: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/PbcutilUnitTest.xml" 38: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pbcutil/tests 38: Test timeout computed to be: 30 38: [==========] Running 37 tests from 5 test suites. 38: [----------] Global test environment set-up. 38: [----------] 1 test from ShiftTest 38: [ RUN ] ShiftTest.CoordinateShiftWorks 38: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 38: [----------] 1 test from ShiftTest (0 ms total) 38: 38: [----------] 2 tests from MShift 38: [ RUN ] MShift.shiftsAndUnshifts 38: [ OK ] MShift.shiftsAndUnshifts (0 ms) 38: [ RUN ] MShift.shiftsAndUnshiftsSelf 38: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 38: [----------] 2 tests from MShift (0 ms total) 38: 38: [----------] 5 tests from PbcTest 38: [ RUN ] PbcTest.CalcShiftsWorks 38: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 38: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 38: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 38: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 38: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 38: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 38: [----------] 5 tests from PbcTest (0 ms total) 38: 38: [----------] 2 tests from PbcEnumsTest 38: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 38: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 38: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 38: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 38: [----------] 2 tests from PbcEnumsTest (0 ms total) 38: 38: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (5 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 38: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (9 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 37 tests from 5 test suites ran. (10 ms total) 38: [ PASSED ] 37 tests. 38/87 Test #38: PbcutilUnitTest ........................... Passed 0.08 sec test 39 Start 39: RandomUnitTests 39: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/RandomUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/random/tests 39: Test timeout computed to be: 30 39: [==========] Running 44 tests from 10 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ExponentialDistributionTest 39: [ RUN ] ExponentialDistributionTest.Output 39: [ OK ] ExponentialDistributionTest.Output (4 ms) 39: [ RUN ] ExponentialDistributionTest.Logical 39: [ OK ] ExponentialDistributionTest.Logical (0 ms) 39: [ RUN ] ExponentialDistributionTest.Reset 39: [ OK ] ExponentialDistributionTest.Reset (0 ms) 39: [ RUN ] ExponentialDistributionTest.AltParam 39: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from ExponentialDistributionTest (5 ms total) 39: 39: [----------] 4 tests from GammaDistributionTest 39: [ RUN ] GammaDistributionTest.Output 39: [ OK ] GammaDistributionTest.Output (0 ms) 39: [ RUN ] GammaDistributionTest.Logical 39: [ OK ] GammaDistributionTest.Logical (0 ms) 39: [ RUN ] GammaDistributionTest.Reset 39: [ OK ] GammaDistributionTest.Reset (0 ms) 39: [ RUN ] GammaDistributionTest.AltParam 39: [ OK ] GammaDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from GammaDistributionTest (0 ms total) 39: 39: [----------] 4 tests from NormalDistributionTest 39: [ RUN ] NormalDistributionTest.Output 39: [ OK ] NormalDistributionTest.Output (0 ms) 39: [ RUN ] NormalDistributionTest.Logical 39: [ OK ] NormalDistributionTest.Logical (0 ms) 39: [ RUN ] NormalDistributionTest.Reset 39: [ OK ] NormalDistributionTest.Reset (0 ms) 39: [ RUN ] NormalDistributionTest.AltParam 39: [ OK ] NormalDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from NormalDistributionTest (0 ms total) 39: 39: [----------] 1 test from SeedTest 39: [ RUN ] SeedTest.makeRandomSeed 39: [ OK ] SeedTest.makeRandomSeed (0 ms) 39: [----------] 1 test from SeedTest (0 ms total) 39: 39: [----------] 6 tests from TabulatedNormalDistributionTest 39: [ RUN ] TabulatedNormalDistributionTest.Output14 39: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Output16 39: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 39: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Logical 39: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Reset 39: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.AltParam 39: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 39: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 39: 39: [----------] 1 test from TabulatedNormalDistributionTableTest 39: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 39: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 39: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 39: 39: [----------] 6 tests from ThreeFry2x64Test 39: [ RUN ] ThreeFry2x64Test.Logical 39: [ OK ] ThreeFry2x64Test.Logical (0 ms) 39: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 39: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 39: [ RUN ] ThreeFry2x64Test.Reseed 39: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 39: [ RUN ] ThreeFry2x64Test.Discard 39: [ OK ] ThreeFry2x64Test.Discard (0 ms) 39: [ RUN ] ThreeFry2x64Test.InvalidCounter 39: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 39: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 39: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 39: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 39: 39: [----------] 4 tests from UniformIntDistributionTest 39: [ RUN ] UniformIntDistributionTest.Output 39: [ OK ] UniformIntDistributionTest.Output (0 ms) 39: [ RUN ] UniformIntDistributionTest.Logical 39: [ OK ] UniformIntDistributionTest.Logical (0 ms) 39: [ RUN ] UniformIntDistributionTest.Reset 39: [ OK ] UniformIntDistributionTest.Reset (0 ms) 39: [ RUN ] UniformIntDistributionTest.AltParam 39: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 39: 39: [----------] 5 tests from UniformRealDistributionTest 39: [ RUN ] UniformRealDistributionTest.GenerateCanonical 39: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 39: [ RUN ] UniformRealDistributionTest.Output 39: [ OK ] UniformRealDistributionTest.Output (0 ms) 39: [ RUN ] UniformRealDistributionTest.Logical 39: [ OK ] UniformRealDistributionTest.Logical (0 ms) 39: [ RUN ] UniformRealDistributionTest.Reset 39: [ OK ] UniformRealDistributionTest.Reset (0 ms) 39: [ RUN ] UniformRealDistributionTest.AltParam 39: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 39: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 39: 39: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 39: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 44 tests from 10 test suites ran. (7 ms total) 39: [ PASSED ] 44 tests. 39/87 Test #39: RandomUnitTests ........................... Passed 0.04 sec test 40 Start 40: RestraintTests 40: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/RestraintTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/restraint/tests 40: Test timeout computed to be: 30 40: [==========] Running 1 test from 1 test suite. 40: [----------] Global test environment set-up. 40: [----------] 1 test from RestraintManager 40: [ RUN ] RestraintManager.restraintList 40: [ OK ] RestraintManager.restraintList (0 ms) 40: [----------] 1 test from RestraintManager (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 1 test from 1 test suite ran. (0 ms total) 40: [ PASSED ] 1 test. 40/87 Test #40: RestraintTests ............................ Passed 0.03 sec test 41 Start 41: TableUnitTests 41: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TableUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tables/tests 41: Test timeout computed to be: 30 41: [==========] Running 20 tests from 2 test suites. 41: [----------] Global test environment set-up. 41: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 41: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 41: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 41: [ RUN ] SplineTableTest/0.Sinc 41: [ OK ] SplineTableTest/0.Sinc (0 ms) 41: [ RUN ] SplineTableTest/0.LJ12 41: [ OK ] SplineTableTest/0.LJ12 (13 ms) 41: [ RUN ] SplineTableTest/0.PmeCorrection 41: [ OK ] SplineTableTest/0.PmeCorrection (12 ms) 41: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 41: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 41: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 41: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 41: [ RUN ] SplineTableTest/0.TwoFunctions 41: [ OK ] SplineTableTest/0.TwoFunctions (29 ms) 41: [ RUN ] SplineTableTest/0.ThreeFunctions 41: [ OK ] SplineTableTest/0.ThreeFunctions (42 ms) 41: [ RUN ] SplineTableTest/0.Simd 41: [ OK ] SplineTableTest/0.Simd (2 ms) 41: [ RUN ] SplineTableTest/0.SimdTwoFunctions 41: [ OK ] SplineTableTest/0.SimdTwoFunctions (24 ms) 41: [----------] 10 tests from SplineTableTest/0 (125 ms total) 41: 41: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 41: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 41: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 41: [ RUN ] SplineTableTest/1.Sinc 41: [ OK ] SplineTableTest/1.Sinc (4 ms) 41: [ RUN ] SplineTableTest/1.LJ12 41: [ OK ] SplineTableTest/1.LJ12 (0 ms) 41: [ RUN ] SplineTableTest/1.PmeCorrection 41: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 41: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 41: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 41: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 41: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 41: [ RUN ] SplineTableTest/1.TwoFunctions 41: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 41: [ RUN ] SplineTableTest/1.ThreeFunctions 41: [ OK ] SplineTableTest/1.ThreeFunctions (11 ms) 41: [ RUN ] SplineTableTest/1.Simd 41: [ OK ] SplineTableTest/1.Simd (0 ms) 41: [ RUN ] SplineTableTest/1.SimdTwoFunctions 41: [ OK ] SplineTableTest/1.SimdTwoFunctions (1 ms) 41: [----------] 10 tests from SplineTableTest/1 (20 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 20 tests from 2 test suites ran. (146 ms total) 41: [ PASSED ] 20 tests. 41/87 Test #41: TableUnitTests ............................ Passed 0.19 sec test 42 Start 42: TaskAssignmentUnitTests 42: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/taskassignment/tests 42: Test timeout computed to be: 30 42: [==========] Running 3 tests from 2 test suites. 42: [----------] Global test environment set-up. 42: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 42: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 42: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 42: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 42: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 42: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 42: 42: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 42: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 42: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 42: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 3 tests from 2 test suites ran. (0 ms total) 42: [ PASSED ] 3 tests. 42/87 Test #42: TaskAssignmentUnitTests ................... Passed 0.04 sec test 43 Start 43: GmxTimingTests 43: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxTimingTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/timing/tests 43: Test timeout computed to be: 30 43: [==========] Running 6 tests from 1 test suite. 43: [----------] Global test environment set-up. 43: [----------] 6 tests from TimingTest 43: [ RUN ] TimingTest.ElementCountingWorks 43: [ OK ] TimingTest.ElementCountingWorks (0 ms) 43: [ RUN ] TimingTest.ElementNoCountingWorks 43: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 43: [ RUN ] TimingTest.SubElementCountingWorks 43: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 43: [ RUN ] TimingTest.SubElementNoCountingWorks 43: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 43: [ RUN ] TimingTest.RunWallCycle 43: [ OK ] TimingTest.RunWallCycle (5 ms) 43: [ RUN ] TimingTest.RunWallCycleSub 43: [ OK ] TimingTest.RunWallCycleSub (0 ms) 43: [----------] 6 tests from TimingTest (6 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 6 tests from 1 test suite ran. (6 ms total) 43: [ PASSED ] 6 tests. 43/87 Test #43: GmxTimingTests ............................ Passed 0.03 sec test 44 Start 44: TopologyTest 44: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TopologyTest.xml" 44: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/topology/tests 44: Test timeout computed to be: 30 44: [==========] Running 153 tests from 10 test suites. 44: [----------] Global test environment set-up. 44: [----------] 3 tests from PdbAtomEntryTest 44: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 44: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 44: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 44: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 44: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 44: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 44: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 44: 44: [----------] 3 tests from ExclusionBlockTest 44: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 44: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 44: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 44: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 44: [ RUN ] ExclusionBlockTest.MergeExclusions 44: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 44: [----------] 3 tests from ExclusionBlockTest (0 ms total) 44: 44: [----------] 6 tests from InteractionListTest 44: [ RUN ] InteractionListTest.EmptyWorks 44: [ OK ] InteractionListTest.EmptyWorks (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionArray 44: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 44: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionPointer 44: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 44: [ RUN ] InteractionListTest.CanAddListToOtherList 44: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 44: [ RUN ] InteractionListTest.ClearingWorks 44: [ OK ] InteractionListTest.ClearingWorks (0 ms) 44: [----------] 6 tests from InteractionListTest (0 ms total) 44: 44: [----------] 3 tests from IndexTest 44: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.AnalyseWorksDefaultGroups (10 ms) 44: [ RUN ] IndexTest.WriteIndexWorks 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.WriteIndexWorks (7 ms) 44: [ RUN ] IndexTest.WriteAndReadIndexWorks 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.WriteAndReadIndexWorks (8 ms) 44: [----------] 3 tests from IndexTest (26 ms total) 44: 44: [----------] 4 tests from MtopTest 44: [ RUN ] MtopTest.RangeBasedLoop 44: [ OK ] MtopTest.RangeBasedLoop (0 ms) 44: [ RUN ] MtopTest.Operators 44: [ OK ] MtopTest.Operators (0 ms) 44: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 44: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 44: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 44: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 44: [----------] 4 tests from MtopTest (0 ms total) 44: 44: [----------] 2 tests from IListRangeTest 44: [ RUN ] IListRangeTest.RangeBasedLoopWorks 44: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 44: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 44: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 44: [----------] 2 tests from IListRangeTest (0 ms total) 44: 44: [----------] 13 tests from StringTableTest 44: [ RUN ] StringTableTest.AddSingleEntry 44: [ OK ] StringTableTest.AddSingleEntry (6 ms) 44: [ RUN ] StringTableTest.CanAccessWithAt 44: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 44: [ RUN ] StringTableTest.CanAccessWithBracket 44: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 44: [ RUN ] StringTableTest.ThrowsOutOfRange 44: [ OK ] StringTableTest.ThrowsOutOfRange (4 ms) 44: [ RUN ] StringTableTest.StringCompareIsCorrect 44: [ OK ] StringTableTest.StringCompareIsCorrect (3 ms) 44: [ RUN ] StringTableTest.AddTwoDistinctEntries 44: [ OK ] StringTableTest.AddTwoDistinctEntries (3 ms) 44: [ RUN ] StringTableTest.TryToAddDuplicates 44: [ OK ] StringTableTest.TryToAddDuplicates (4 ms) 44: [ RUN ] StringTableTest.AddLargeNumberOfEntries 44: [ OK ] StringTableTest.AddLargeNumberOfEntries (3 ms) 44: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 44: [ OK ] StringTableTest.NoDuplicatesInLargeTable (3 ms) 44: [ RUN ] StringTableTest.CanWriteToBuffer 44: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 44: [ RUN ] StringTableTest.Roundtrip 44: [ OK ] StringTableTest.Roundtrip (0 ms) 44: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 44: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 44: [ RUN ] StringTableTest.CanCopyToLegacyTable 44: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 44: [----------] 13 tests from StringTableTest (30 ms total) 44: 44: [----------] 6 tests from LegacySymtabTest 44: [ RUN ] LegacySymtabTest.EmptyOnOpen 44: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 44: [ RUN ] LegacySymtabTest.AddSingleEntry 44: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 44: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 44: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 44: [ RUN ] LegacySymtabTest.TryToAddDuplicates 44: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 44: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 44: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 44: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 44: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (7 ms) 44: [----------] 6 tests from LegacySymtabTest (7 ms total) 44: 44: [----------] 5 tests from TopSortTest 44: [ RUN ] TopSortTest.WorksOnEmptyIdef 44: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 44: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 44: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 44: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 44: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 44: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 44: [----------] 5 tests from TopSortTest (0 ms total) 44: 44: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (7 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (4 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (5 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (7 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (5 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (7 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (5 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (5 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (3 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (6 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (5 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (5 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (7 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (1 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 44: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (142 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 153 tests from 10 test suites ran. (207 ms total) 44: [ PASSED ] 153 tests. 44: 44: YOU HAVE 1 DISABLED TEST 44: 44/87 Test #44: TopologyTest .............................. Passed 0.24 sec test 45 Start 45: PullTest 45: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/PullTest.xml" 45: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/pulling/tests 45: Test timeout computed to be: 30 45: [==========] Running 10 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from PullTest 45: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 45: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 45: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 45: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 45: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 45: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 45: [ RUN ] PullTest.TransformationCoordSimple 45: [ OK ] PullTest.TransformationCoordSimple (24 ms) 45: [ RUN ] PullTest.TransformationCoordAdvanced 45: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 45: [ RUN ] PullTest.TransformationCoordTime 45: [ OK ] PullTest.TransformationCoordTime (0 ms) 45: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 45: [ OK ] PullTest.TransformationCoordTimeNotAllowed (13 ms) 45: [ RUN ] PullTest.TransformationCoordDummyExpression 45: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 45: [----------] 10 tests from PullTest (38 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 10 tests from 1 test suite ran. (38 ms total) 45: [ PASSED ] 10 tests. 45/87 Test #45: PullTest .................................. Passed 0.07 sec test 46 Start 46: SimdUnitTests 46: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/SimdUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/simd/tests 46: Test timeout computed to be: 30 46: [==========] Running 288 tests from 22 test suites. 46: [----------] Global test environment set-up. 46: [----------] 9 tests from SimdBootstrapTest 46: [ RUN ] SimdBootstrapTest.loadStore 46: [ OK ] SimdBootstrapTest.loadStore (0 ms) 46: [ RUN ] SimdBootstrapTest.loadU 46: [ OK ] SimdBootstrapTest.loadU (0 ms) 46: [ RUN ] SimdBootstrapTest.storeU 46: [ OK ] SimdBootstrapTest.storeU (0 ms) 46: [ RUN ] SimdBootstrapTest.loadStoreI 46: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 46: [ RUN ] SimdBootstrapTest.loadUI 46: [ OK ] SimdBootstrapTest.loadUI (0 ms) 46: [ RUN ] SimdBootstrapTest.storeUI 46: [ OK ] SimdBootstrapTest.storeUI (0 ms) 46: [ RUN ] SimdBootstrapTest.simd4LoadStore 46: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 46: [ RUN ] SimdBootstrapTest.simd4LoadU 46: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 46: [ RUN ] SimdBootstrapTest.simd4StoreU 46: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 46: [----------] 9 tests from SimdBootstrapTest (0 ms total) 46: 46: [----------] 41 tests from SimdScalarTest 46: [ RUN ] SimdScalarTest.load 46: [ OK ] SimdScalarTest.load (0 ms) 46: [ RUN ] SimdScalarTest.loadU 46: [ OK ] SimdScalarTest.loadU (0 ms) 46: [ RUN ] SimdScalarTest.store 46: [ OK ] SimdScalarTest.store (0 ms) 46: [ RUN ] SimdScalarTest.storeU 46: [ OK ] SimdScalarTest.storeU (0 ms) 46: [ RUN ] SimdScalarTest.setZero 46: [ OK ] SimdScalarTest.setZero (0 ms) 46: [ RUN ] SimdScalarTest.andNot 46: [ OK ] SimdScalarTest.andNot (0 ms) 46: [ RUN ] SimdScalarTest.fma 46: [ OK ] SimdScalarTest.fma (0 ms) 46: [ RUN ] SimdScalarTest.fms 46: [ OK ] SimdScalarTest.fms (0 ms) 46: [ RUN ] SimdScalarTest.fnma 46: [ OK ] SimdScalarTest.fnma (0 ms) 46: [ RUN ] SimdScalarTest.fnms 46: [ OK ] SimdScalarTest.fnms (0 ms) 46: [ RUN ] SimdScalarTest.maskAdd 46: [ OK ] SimdScalarTest.maskAdd (0 ms) 46: [ RUN ] SimdScalarTest.maskzMul 46: [ OK ] SimdScalarTest.maskzMul (0 ms) 46: [ RUN ] SimdScalarTest.maskzFma 46: [ OK ] SimdScalarTest.maskzFma (0 ms) 46: [ RUN ] SimdScalarTest.abs 46: [ OK ] SimdScalarTest.abs (0 ms) 46: [ RUN ] SimdScalarTest.max 46: [ OK ] SimdScalarTest.max (0 ms) 46: [ RUN ] SimdScalarTest.min 46: [ OK ] SimdScalarTest.min (0 ms) 46: [ RUN ] SimdScalarTest.round 46: [ OK ] SimdScalarTest.round (0 ms) 46: [ RUN ] SimdScalarTest.trunc 46: [ OK ] SimdScalarTest.trunc (0 ms) 46: [ RUN ] SimdScalarTest.reduce 46: [ OK ] SimdScalarTest.reduce (0 ms) 46: [ RUN ] SimdScalarTest.testBits 46: [ OK ] SimdScalarTest.testBits (0 ms) 46: [ RUN ] SimdScalarTest.anyTrue 46: [ OK ] SimdScalarTest.anyTrue (0 ms) 46: [ RUN ] SimdScalarTest.selectByMask 46: [ OK ] SimdScalarTest.selectByMask (0 ms) 46: [ RUN ] SimdScalarTest.selectByNotMask 46: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 46: [ RUN ] SimdScalarTest.blend 46: [ OK ] SimdScalarTest.blend (0 ms) 46: [ RUN ] SimdScalarTest.cvtR2I 46: [ OK ] SimdScalarTest.cvtR2I (0 ms) 46: [ RUN ] SimdScalarTest.cvttR2I 46: [ OK ] SimdScalarTest.cvttR2I (0 ms) 46: [ RUN ] SimdScalarTest.cvtI2R 46: [ OK ] SimdScalarTest.cvtI2R (0 ms) 46: [ RUN ] SimdScalarTest.cvtF2D 46: [ OK ] SimdScalarTest.cvtF2D (0 ms) 46: [ RUN ] SimdScalarTest.cvtD2D 46: [ OK ] SimdScalarTest.cvtD2D (0 ms) 46: [ RUN ] SimdScalarTest.loadI 46: [ OK ] SimdScalarTest.loadI (0 ms) 46: [ RUN ] SimdScalarTest.loadUI 46: [ OK ] SimdScalarTest.loadUI (0 ms) 46: [ RUN ] SimdScalarTest.storeI 46: [ OK ] SimdScalarTest.storeI (0 ms) 46: [ RUN ] SimdScalarTest.storeUI 46: [ OK ] SimdScalarTest.storeUI (0 ms) 46: [ RUN ] SimdScalarTest.andNotI 46: [ OK ] SimdScalarTest.andNotI (0 ms) 46: [ RUN ] SimdScalarTest.testBitsI 46: [ OK ] SimdScalarTest.testBitsI (0 ms) 46: [ RUN ] SimdScalarTest.selectByMaskI 46: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 46: [ RUN ] SimdScalarTest.selectByNotMaskI 46: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 46: [ RUN ] SimdScalarTest.blendI 46: [ OK ] SimdScalarTest.blendI (0 ms) 46: [ RUN ] SimdScalarTest.cvtB2IB 46: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 46: [ RUN ] SimdScalarTest.cvtIB2B 46: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 46: [ RUN ] SimdScalarTest.expandScalarsToTriplets 46: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 46: [----------] 41 tests from SimdScalarTest (0 ms total) 46: 46: [----------] 8 tests from SimdScalarUtilTest 46: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 46: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 46: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 46: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 46: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 46: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 46: 46: [----------] 37 tests from SimdScalarMathTest 46: [ RUN ] SimdScalarMathTest.copysign 46: [ OK ] SimdScalarMathTest.copysign (0 ms) 46: [ RUN ] SimdScalarMathTest.invsqrtPair 46: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 46: [ RUN ] SimdScalarMathTest.inv 46: [ OK ] SimdScalarMathTest.inv (0 ms) 46: [ RUN ] SimdScalarMathTest.maskzInvsqrt 46: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 46: [ RUN ] SimdScalarMathTest.log 46: [ OK ] SimdScalarMathTest.log (0 ms) 46: [ RUN ] SimdScalarMathTest.exp2 46: [ OK ] SimdScalarMathTest.exp2 (0 ms) 46: [ RUN ] SimdScalarMathTest.exp 46: [ OK ] SimdScalarMathTest.exp (0 ms) 46: [ RUN ] SimdScalarMathTest.erf 46: [ OK ] SimdScalarMathTest.erf (0 ms) 46: [ RUN ] SimdScalarMathTest.erfc 46: [ OK ] SimdScalarMathTest.erfc (0 ms) 46: [ RUN ] SimdScalarMathTest.sincos 46: [ OK ] SimdScalarMathTest.sincos (0 ms) 46: [ RUN ] SimdScalarMathTest.sin 46: [ OK ] SimdScalarMathTest.sin (0 ms) 46: [ RUN ] SimdScalarMathTest.cos 46: [ OK ] SimdScalarMathTest.cos (0 ms) 46: [ RUN ] SimdScalarMathTest.tan 46: [ OK ] SimdScalarMathTest.tan (0 ms) 46: [ RUN ] SimdScalarMathTest.asin 46: [ OK ] SimdScalarMathTest.asin (0 ms) 46: [ RUN ] SimdScalarMathTest.acos 46: [ OK ] SimdScalarMathTest.acos (0 ms) 46: [ RUN ] SimdScalarMathTest.atan 46: [ OK ] SimdScalarMathTest.atan (0 ms) 46: [ RUN ] SimdScalarMathTest.atan2 46: [ OK ] SimdScalarMathTest.atan2 (0 ms) 46: [ RUN ] SimdScalarMathTest.pmeForceCorrection 46: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 46: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 46: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 46: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 46: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.invSingleAccuracy 46: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 46: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.logSingleAccuracy 46: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 46: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.expSingleAccuracy 46: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 46: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 46: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 46: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 46: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 46: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 46: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 46: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 46: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 46: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 46: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 46: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 46: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 46: [----------] 37 tests from SimdScalarMathTest (0 ms total) 46: 46: [----------] 1 test from SimdTest 46: [ RUN ] SimdTest.GmxAligned 46: [ OK ] SimdTest.GmxAligned (0 ms) 46: [----------] 1 test from SimdTest (0 ms total) 46: 46: [----------] 42 tests from SimdFloatingpointTest 46: [ RUN ] SimdFloatingpointTest.setZero 46: [ OK ] SimdFloatingpointTest.setZero (0 ms) 46: [ RUN ] SimdFloatingpointTest.set 46: [ OK ] SimdFloatingpointTest.set (0 ms) 46: [ RUN ] SimdFloatingpointTest.add 46: [ OK ] SimdFloatingpointTest.add (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskAdd 46: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 46: [ RUN ] SimdFloatingpointTest.sub 46: [ OK ] SimdFloatingpointTest.sub (0 ms) 46: [ RUN ] SimdFloatingpointTest.mul 46: [ OK ] SimdFloatingpointTest.mul (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzMul 46: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 46: [ RUN ] SimdFloatingpointTest.fma 46: [ OK ] SimdFloatingpointTest.fma (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzFma 46: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 46: [ RUN ] SimdFloatingpointTest.fms 46: [ OK ] SimdFloatingpointTest.fms (0 ms) 46: [ RUN ] SimdFloatingpointTest.fnma 46: [ OK ] SimdFloatingpointTest.fnma (0 ms) 46: [ RUN ] SimdFloatingpointTest.fnms 46: [ OK ] SimdFloatingpointTest.fnms (0 ms) 46: [ RUN ] SimdFloatingpointTest.abs 46: [ OK ] SimdFloatingpointTest.abs (0 ms) 46: [ RUN ] SimdFloatingpointTest.neg 46: [ OK ] SimdFloatingpointTest.neg (0 ms) 46: [ RUN ] SimdFloatingpointTest.and 46: [ OK ] SimdFloatingpointTest.and (0 ms) 46: [ RUN ] SimdFloatingpointTest.or 46: [ OK ] SimdFloatingpointTest.or (0 ms) 46: [ RUN ] SimdFloatingpointTest.xor 46: [ OK ] SimdFloatingpointTest.xor (0 ms) 46: [ RUN ] SimdFloatingpointTest.andNot 46: [ OK ] SimdFloatingpointTest.andNot (0 ms) 46: [ RUN ] SimdFloatingpointTest.max 46: [ OK ] SimdFloatingpointTest.max (0 ms) 46: [ RUN ] SimdFloatingpointTest.min 46: [ OK ] SimdFloatingpointTest.min (0 ms) 46: [ RUN ] SimdFloatingpointTest.round 46: [ OK ] SimdFloatingpointTest.round (0 ms) 46: [ RUN ] SimdFloatingpointTest.roundMode 46: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 46: [ RUN ] SimdFloatingpointTest.trunc 46: [ OK ] SimdFloatingpointTest.trunc (0 ms) 46: [ RUN ] SimdFloatingpointTest.frexp 46: [ OK ] SimdFloatingpointTest.frexp (0 ms) 46: [ RUN ] SimdFloatingpointTest.ldexp 46: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 46: [ RUN ] SimdFloatingpointTest.rsqrt 46: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzRsqrt 46: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 46: [ RUN ] SimdFloatingpointTest.rcp 46: [ OK ] SimdFloatingpointTest.rcp (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzRcp 46: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 46: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 46: [ RUN ] SimdFloatingpointTest.selectByNotMask 46: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpNe 46: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpLe 46: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpLt 46: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 46: [ RUN ] SimdFloatingpointTest.testBits 46: [ OK ] SimdFloatingpointTest.testBits (0 ms) 46: [ RUN ] SimdFloatingpointTest.andB 46: [ OK ] SimdFloatingpointTest.andB (0 ms) 46: [ RUN ] SimdFloatingpointTest.orB 46: [ OK ] SimdFloatingpointTest.orB (0 ms) 46: [ RUN ] SimdFloatingpointTest.anyTrueB 46: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 46: [ RUN ] SimdFloatingpointTest.blend 46: [ OK ] SimdFloatingpointTest.blend (0 ms) 46: [ RUN ] SimdFloatingpointTest.reduce 46: [ OK ] SimdFloatingpointTest.reduce (0 ms) 46: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 46: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 46: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 46: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 46: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 46: 46: [----------] 16 tests from SimdFloatingpointUtilTest 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 46: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 46: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 46: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 46: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 46: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 46: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 46: 46: [----------] 23 tests from SimdIntegerTest 46: [ RUN ] SimdIntegerTest.setZero 46: [ OK ] SimdIntegerTest.setZero (0 ms) 46: [ RUN ] SimdIntegerTest.set 46: [ OK ] SimdIntegerTest.set (0 ms) 46: [ RUN ] SimdIntegerTest.add 46: [ OK ] SimdIntegerTest.add (0 ms) 46: [ RUN ] SimdIntegerTest.sub 46: [ OK ] SimdIntegerTest.sub (0 ms) 46: [ RUN ] SimdIntegerTest.mul 46: [ OK ] SimdIntegerTest.mul (0 ms) 46: [ RUN ] SimdIntegerTest.and 46: [ OK ] SimdIntegerTest.and (0 ms) 46: [ RUN ] SimdIntegerTest.andNot 46: [ OK ] SimdIntegerTest.andNot (0 ms) 46: [ RUN ] SimdIntegerTest.or 46: [ OK ] SimdIntegerTest.or (0 ms) 46: [ RUN ] SimdIntegerTest.xor 46: [ OK ] SimdIntegerTest.xor (0 ms) 46: [ RUN ] SimdIntegerTest.extract 46: [ OK ] SimdIntegerTest.extract (0 ms) 46: [ RUN ] SimdIntegerTest.cvtR2I 46: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 46: [ RUN ] SimdIntegerTest.cvttR2I 46: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 46: [ RUN ] SimdIntegerTest.cvtI2R 46: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 46: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 46: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 46: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 46: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 46: [ RUN ] SimdIntegerTest.cmpLt 46: [ OK ] SimdIntegerTest.cmpLt (0 ms) 46: [ RUN ] SimdIntegerTest.testBits 46: [ OK ] SimdIntegerTest.testBits (0 ms) 46: [ RUN ] SimdIntegerTest.andB 46: [ OK ] SimdIntegerTest.andB (0 ms) 46: [ RUN ] SimdIntegerTest.orB 46: [ OK ] SimdIntegerTest.orB (0 ms) 46: [ RUN ] SimdIntegerTest.anyTrue 46: [ OK ] SimdIntegerTest.anyTrue (0 ms) 46: [ RUN ] SimdIntegerTest.blend 46: [ OK ] SimdIntegerTest.blend (0 ms) 46: [ RUN ] SimdIntegerTest.cvtB2IB 46: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 46: [ RUN ] SimdIntegerTest.cvtIB2B 46: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 46: [----------] 23 tests from SimdIntegerTest (0 ms total) 46: 46: [----------] 56 tests from SimdMathTest 46: [ RUN ] SimdMathTest.generateTestPointsFloat 46: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 46: [ RUN ] SimdMathTest.copysign 46: [ OK ] SimdMathTest.copysign (0 ms) 46: [ RUN ] SimdMathTest.invsqrt 46: [ OK ] SimdMathTest.invsqrt (0 ms) 46: [ RUN ] SimdMathTest.maskzInvsqrt 46: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 46: [ RUN ] SimdMathTest.invsqrtPair 46: [ OK ] SimdMathTest.invsqrtPair (0 ms) 46: [ RUN ] SimdMathTest.sqrt 46: [ OK ] SimdMathTest.sqrt (0 ms) 46: [ RUN ] SimdMathTest.sqrtUnsafe 46: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 46: [ RUN ] SimdMathTest.inv 46: [ OK ] SimdMathTest.inv (0 ms) 46: [ RUN ] SimdMathTest.maskzInv 46: [ OK ] SimdMathTest.maskzInv (0 ms) 46: [ RUN ] SimdMathTest.cbrt 46: [ OK ] SimdMathTest.cbrt (0 ms) 46: [ RUN ] SimdMathTest.invcbrt 46: [ OK ] SimdMathTest.invcbrt (0 ms) 46: [ RUN ] SimdMathTest.log2 46: [ OK ] SimdMathTest.log2 (7 ms) 46: [ RUN ] SimdMathTest.log 46: [ OK ] SimdMathTest.log (0 ms) 46: [ RUN ] SimdMathTest.exp2 46: [ OK ] SimdMathTest.exp2 (0 ms) 46: [ RUN ] SimdMathTest.exp2Unsafe 46: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 46: [ RUN ] SimdMathTest.exp 46: [ OK ] SimdMathTest.exp (0 ms) 46: [ RUN ] SimdMathTest.expUnsafe 46: [ OK ] SimdMathTest.expUnsafe (0 ms) 46: [ RUN ] SimdMathTest.pow 46: [ OK ] SimdMathTest.pow (0 ms) 46: [ RUN ] SimdMathTest.powUnsafe 46: [ OK ] SimdMathTest.powUnsafe (0 ms) 46: [ RUN ] SimdMathTest.erf 46: [ OK ] SimdMathTest.erf (0 ms) 46: [ RUN ] SimdMathTest.erfc 46: [ OK ] SimdMathTest.erfc (0 ms) 46: [ RUN ] SimdMathTest.sin 46: [ OK ] SimdMathTest.sin (0 ms) 46: [ RUN ] SimdMathTest.cos 46: [ OK ] SimdMathTest.cos (0 ms) 46: [ RUN ] SimdMathTest.tan 46: [ OK ] SimdMathTest.tan (0 ms) 46: [ RUN ] SimdMathTest.asin 46: [ OK ] SimdMathTest.asin (0 ms) 46: [ RUN ] SimdMathTest.acos 46: [ OK ] SimdMathTest.acos (0 ms) 46: [ RUN ] SimdMathTest.atan 46: [ OK ] SimdMathTest.atan (0 ms) 46: [ RUN ] SimdMathTest.atan2 46: [ OK ] SimdMathTest.atan2 (0 ms) 46: [ RUN ] SimdMathTest.pmeForceCorrection 46: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 46: [ RUN ] SimdMathTest.pmePotentialCorrection 46: [ OK ] SimdMathTest.pmePotentialCorrection (8 ms) 46: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 46: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 46: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sqrtSingleAccuracy 46: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.invSingleAccuracy 46: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.cbrtSingleAccuracy 46: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 46: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.log2SingleAccuracy 46: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.logSingleAccuracy 46: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.exp2SingleAccuracy 46: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 46: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.expSingleAccuracy 46: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) 46: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.powSingleAccuracy 46: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.erfSingleAccuracy 46: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.erfcSingleAccuracy 46: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sinSingleAccuracy 46: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.cosSingleAccuracy 46: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.tanSingleAccuracy 46: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.asinSingleAccuracy 46: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.acosSingleAccuracy 46: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.atanSingleAccuracy 46: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.atan2SingleAccuracy 46: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 46: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (4 ms) 46: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 46: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 46: [----------] 56 tests from SimdMathTest (35 ms total) 46: 46: [----------] 1 test from EmptyArrayRefTest 46: [ RUN ] EmptyArrayRefTest.IsEmpty 46: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 46: [----------] 1 test from EmptyArrayRefTest (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 46: 46: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefReadWriteTest/0.Assignment 46: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 46: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 46: 46: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefReadWriteTest/1.Assignment 46: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 46: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 46: 46: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefArithmeticTest/0.Basic 46: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 46: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 46: 46: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefArithmeticTest/1.Basic 46: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 46: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 46: 46: [----------] 3 tests from SimdVectorOperationsTest 46: [ RUN ] SimdVectorOperationsTest.iprod 46: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 46: [ RUN ] SimdVectorOperationsTest.norm2 46: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 46: [ RUN ] SimdVectorOperationsTest.cprod 46: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 46: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 46: 46: [----------] 32 tests from Simd4FloatingpointTest 46: [ RUN ] Simd4FloatingpointTest.setZero 46: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 46: [ RUN ] Simd4FloatingpointTest.set 46: [ OK ] Simd4FloatingpointTest.set (0 ms) 46: [ RUN ] Simd4FloatingpointTest.add 46: [ OK ] Simd4FloatingpointTest.add (0 ms) 46: [ RUN ] Simd4FloatingpointTest.sub 46: [ OK ] Simd4FloatingpointTest.sub (0 ms) 46: [ RUN ] Simd4FloatingpointTest.mul 46: [ OK ] Simd4FloatingpointTest.mul (0 ms) 46: [ RUN ] Simd4FloatingpointTest.fma 46: [ OK ] Simd4FloatingpointTest.fma (0 ms) 46: [ RUN ] Simd4FloatingpointTest.fms 46: [ OK ] Simd4FloatingpointTest.fms (0 ms) 46: [ RUN ] Simd4FloatingpointTest.fnma 46: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 46: [ RUN ] Simd4FloatingpointTest.fnms 46: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 46: [ RUN ] Simd4FloatingpointTest.abs 46: [ OK ] Simd4FloatingpointTest.abs (0 ms) 46: [ RUN ] Simd4FloatingpointTest.neg 46: [ OK ] Simd4FloatingpointTest.neg (0 ms) 46: [ RUN ] Simd4FloatingpointTest.and 46: [ OK ] Simd4FloatingpointTest.and (0 ms) 46: [ RUN ] Simd4FloatingpointTest.or 46: [ OK ] Simd4FloatingpointTest.or (0 ms) 46: [ RUN ] Simd4FloatingpointTest.xor 46: [ OK ] Simd4FloatingpointTest.xor (0 ms) 46: [ RUN ] Simd4FloatingpointTest.andNot 46: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 46: [ RUN ] Simd4FloatingpointTest.max 46: [ OK ] Simd4FloatingpointTest.max (0 ms) 46: [ RUN ] Simd4FloatingpointTest.min 46: [ OK ] Simd4FloatingpointTest.min (0 ms) 46: [ RUN ] Simd4FloatingpointTest.round 46: [ OK ] Simd4FloatingpointTest.round (0 ms) 46: [ RUN ] Simd4FloatingpointTest.trunc 46: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 46: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 46: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 46: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 46: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 46: [ RUN ] Simd4FloatingpointTest.selectByNotMask 46: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 46: [ RUN ] Simd4FloatingpointTest.cmpNe 46: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 46: [ RUN ] Simd4FloatingpointTest.cmpLe 46: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 46: [ RUN ] Simd4FloatingpointTest.cmpLt 46: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 46: [ RUN ] Simd4FloatingpointTest.andB 46: [ OK ] Simd4FloatingpointTest.andB (0 ms) 46: [ RUN ] Simd4FloatingpointTest.orB 46: [ OK ] Simd4FloatingpointTest.orB (0 ms) 46: [ RUN ] Simd4FloatingpointTest.anyTrue 46: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 46: [ RUN ] Simd4FloatingpointTest.blend 46: [ OK ] Simd4FloatingpointTest.blend (0 ms) 46: [ RUN ] Simd4FloatingpointTest.reduce 46: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 46: [ RUN ] Simd4FloatingpointTest.dotProduct 46: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 46: [ RUN ] Simd4FloatingpointTest.transpose 46: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 46: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 46: 46: [----------] 2 tests from Simd4MathTest 46: [ RUN ] Simd4MathTest.invsqrt 46: [ OK ] Simd4MathTest.invsqrt (0 ms) 46: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 46: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 46: [----------] 2 tests from Simd4MathTest (0 ms total) 46: 46: [----------] 1 test from Simd4VectorOperationsTest 46: [ RUN ] Simd4VectorOperationsTest.norm2 46: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 46: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 288 tests from 22 test suites ran. (42 ms total) 46: [ PASSED ] 288 tests. 46/87 Test #46: SimdUnitTests ............................. Passed 0.09 sec test 47 Start 47: CompatibilityHelpersTests 47: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/compat/tests 47: Test timeout computed to be: 30 47: [==========] Running 9 tests from 6 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from TemplateMPTest 47: [ RUN ] TemplateMPTest.MpWithIndexInt 47: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexIntBad 47: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexBool 47: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexEnum 47: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 47: [----------] 4 tests from TemplateMPTest (0 ms total) 47: 47: [----------] 1 test from NotNullConstruction 47: [ RUN ] NotNullConstruction.Works 47: [ OK ] NotNullConstruction.Works (0 ms) 47: [----------] 1 test from NotNullConstruction (0 ms total) 47: 47: [----------] 1 test from NotNullCasting 47: [ RUN ] NotNullCasting.Works 47: [ OK ] NotNullCasting.Works (0 ms) 47: [----------] 1 test from NotNullCasting (0 ms total) 47: 47: [----------] 1 test from NotNullAssignment 47: [ RUN ] NotNullAssignment.Works 47: [ OK ] NotNullAssignment.Works (0 ms) 47: [----------] 1 test from NotNullAssignment (0 ms total) 47: 47: [----------] 1 test from MakeNotNull 47: [ RUN ] MakeNotNull.Works 47: [ OK ] MakeNotNull.Works (0 ms) 47: [----------] 1 test from MakeNotNull (0 ms total) 47: 47: [----------] 1 test from NotNull 47: [ RUN ] NotNull.WorksInContainers 47: [ OK ] NotNull.WorksInContainers (0 ms) 47: [----------] 1 test from NotNull (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 9 tests from 6 test suites ran. (0 ms total) 47: [ PASSED ] 9 tests. 47/87 Test #47: CompatibilityHelpersTests ................. Passed 0.04 sec test 48 Start 48: GmxAnaTest 48: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxAnaTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxana/tests 48: Test timeout computed to be: 600 48: [==========] Running 31 tests from 4 test suites. 48: [----------] Global test environment set-up. 48: [----------] 7 tests from Entropy 48: [ RUN ] Entropy.Schlitter_300_NoLinear 48: [ OK ] Entropy.Schlitter_300_NoLinear (6 ms) 48: [ RUN ] Entropy.Schlitter_300_Linear 48: [ OK ] Entropy.Schlitter_300_Linear (3 ms) 48: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 48: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 48: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (4 ms) 48: [ RUN ] Entropy.QuasiHarmonic_200_Linear 48: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 48: [ RUN ] Entropy.EntropyCompare_200_Linear 48: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 48: [ RUN ] Entropy.EntropyCompare_300_Linear 48: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 48: [----------] 7 tests from Entropy (15 ms total) 48: 48: [----------] 2 tests from GmxChiTest 48: [ RUN ] GmxChiTest.gmxchiWorksWithAll 48: Analyzing from residue 1 to residue 11 48: 10 residues with dihedrals found 48: 46 dihedrals found 48: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 48: j after resetting (nr. active dihedrals) = 46 48: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 48: Now calculating transitions... 48: Total number of transitions: 0 48: Now printing out transitions and OPs... 48: Now printing out rotamer occupancies... 48: Now calculating Chi product trajectories... 48: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 48: [ OK ] GmxChiTest.gmxchiWorksWithAll (1911 ms) 48: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 48: Analyzing from residue 2 to residue 6 48: 5 residues with dihedrals found 48: 23 dihedrals found 48: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 48: j after resetting (nr. active dihedrals) = 23 48: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 48: Now calculating transitions... 48: Total number of transitions: 0 48: Now printing out transitions and OPs... 48: Now printing out rotamer occupancies... 48: Now calculating Chi product trajectories... 48: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 48: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (1763 ms) 48: [----------] 2 tests from GmxChiTest (3988 ms total) 48: 48: [----------] 10 tests from MindistTest 48: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistWorksWithSingleAtoms (50 ms) 48: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 2: 'atom3' 48: Selected 3: 'atoms12' 48: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 48: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 48: [ RUN ] MindistTest.mindistPicksUpContacts 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 48: [ RUN ] MindistTest.ngWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.ngWorks (15 ms) 48: [ RUN ] MindistTest.groupWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 3: 'atoms12' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.groupWorks (0 ms) 48: [ RUN ] MindistTest.maxDistWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 2: 'atom3' 48: Selected 3: 'atoms12' 48: [ OK ] MindistTest.maxDistWorks (0 ms) 48: [ RUN ] MindistTest.noPbcWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.noPbcWorks (0 ms) 48: [ RUN ] MindistTest.resPerTimeWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 3: 'atoms12' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.resPerTimeWorks (0 ms) 48: [ RUN ] MindistTest.matrixWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 5: 'atoms123' 48: Special case: making distance matrix between all atoms in group atoms123 48: [ OK ] MindistTest.matrixWorks (0 ms) 48: [----------] 10 tests from MindistTest (69 ms total) 48: 48: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: trr version: GMX_trn_file (single precision) 48: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (17 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (7 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (4 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (23 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (8 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 48: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (29 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (1 ms) 48: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (96 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 31 tests from 4 test suites ran. (4169 ms total) 48: [ PASSED ] 31 tests. 48/87 Test #48: GmxAnaTest ................................ Passed 4.27 sec test 49 Start 49: GmxPreprocessTests 49: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests 49: Test timeout computed to be: 1920 49: [==========] Running 138 tests from 13 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from GenconfTest 49: [ RUN ] GenconfTest.nbox_Works 49: [ OK ] GenconfTest.nbox_Works (37 ms) 49: [ RUN ] GenconfTest.nbox_norenumber_Works 49: [ OK ] GenconfTest.nbox_norenumber_Works (3 ms) 49: [ RUN ] GenconfTest.nbox_dist_Works 49: [ OK ] GenconfTest.nbox_dist_Works (8 ms) 49: [ RUN ] GenconfTest.nbox_rot_Works 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: [ OK ] GenconfTest.nbox_rot_Works (8 ms) 49: [----------] 4 tests from GenconfTest (57 ms total) 49: 49: [----------] 2 tests from GenionTest 49: [ RUN ] GenionTest.HighConcentrationIonPlacement 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 49: buffer. The cluster pair list does have a buffering effect, but choosing 49: a larger rlist might be necessary for good energy conservation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 49: < 0 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: Generating 1-4 interactions: fudge = 0.5 49: Number of degrees of freedom in T-Coupling group rest is 1308.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: Group 0 ( System) has 653 elements 49: Group 1 ( Water) has 648 elements 49: Group 2 ( SOL) has 648 elements 49: Group 3 ( non-Water) has 5 elements 49: Group 4 ( Other) has 5 elements 49: Group 5 ( METH) has 5 elements 49: Select a group: Number of (3-atomic) solvent molecules: 216 49: Using random seed 1997. 49: Replacing solvent molecule 56 (atom 168) with NA 49: Replacing solvent molecule 120 (atom 360) with NA 49: Replacing solvent molecule 182 (atom 546) with NA 49: Replacing solvent molecule 71 (atom 213) with NA 49: Replacing solvent molecule 189 (atom 567) with CL 49: Replacing solvent molecule 54 (atom 162) with CL 49: Replacing solvent molecule 155 (atom 465) with CL 49: Replacing solvent molecule 99 (atom 297) with CL 49: 49: Setting the LD random seed to -67633730 49: 49: Generated 331705 of the 331705 non-bonded parameter combinations 49: 49: Generated 331705 of the 331705 1-4 parameter combinations 49: 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: 49: Excluding 3 bonded neighbours molecule type 'methane' 49: Analysing residue names: 49: There are: 216 Water residues 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: This run will generate roughly 0 Mb of data 49: Will try to add 4 NA ions and 4 CL ions. 49: Select a continuous group of solvent molecules 49: Selected 1: 'Water' 49: [ OK ] GenionTest.HighConcentrationIonPlacement (1027 ms) 49: [ RUN ] GenionTest.NoIonPlacement 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 49: buffer. The cluster pair list does have a buffering effect, but choosing 49: a larger rlist might be necessary for good energy conservation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 49: < 0 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: Generating 1-4 interactions: fudge = 0.5 49: Number of degrees of freedom in T-Coupling group rest is 1308.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: No ions to add, will just copy input configuration. 49: Setting the LD random seed to -524465 49: 49: Generated 331705 of the 331705 non-bonded parameter combinations 49: 49: Generated 331705 of the 331705 1-4 parameter combinations 49: 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: 49: Excluding 3 bonded neighbours molecule type 'methane' 49: Analysing residue names: 49: There are: 216 Water residues 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: This run will generate roughly 0 Mb of data 49: [ OK ] GenionTest.NoIonPlacement (713 ms) 49: [----------] 2 tests from GenionTest (1740 ms total) 49: 49: [----------] 1 test from GenRestrTest 49: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 49: 49: Reading structure file 49: Group 0 ( System) has 156 elements 49: Group 1 ( Protein) has 156 elements 49: Group 2 ( Protein-H) has 75 elements 49: Group 3 ( C-alpha) has 10 elements 49: Group 4 ( Backbone) has 30 elements 49: Group 5 ( MainChain) has 40 elements 49: Group 6 ( MainChain+Cb) has 49 elements 49: Group 7 ( MainChain+H) has 52 elements 49: Group 8 ( SideChain) has 104 elements 49: Group 9 ( SideChain-H) has 35 elements 49: Select a group: Select group to position restrain 49: Selected 3: 'C-alpha' 49: [ OK ] GenRestrTest.SimpleRestraintsGenerated (11 ms) 49: [----------] 1 test from GenRestrTest (11 ms total) 49: 49: [----------] 9 tests from PreprocessingAtomTypesTest 49: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 49: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 49: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 49: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 49: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 49: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 49: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 49: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 49: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 49: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 49: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 49: 49: [----------] 10 tests from PreprocessingBondAtomTypeTest 49: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 49: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 49: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 49: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 49: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 49: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 49: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 49: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 49: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 49: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 49: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 49: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 49: 49: [----------] 1 test from GromppDirectiveTest 49: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 49: Ignoring obsolete mdp entry 'title' 49: Generating 1-4 interactions: fudge = 0.5 49: 49: NOTE 1 [file directives.top, line 44]: 49: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 49: any other atom in the same moleculetype. Although technically this might 49: not cause issues in a simulation, this often means that the user forgot 49: to add a bond/potential/constraint or put multiple molecules in the same 49: moleculetype definition by mistake. Run with -v to get information for 49: each atom. 49: 49: Number of degrees of freedom in T-Coupling group rest is 9.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 49: NVE simulation: will use the initial temperature of 300.000 K for 49: determining the Verlet buffer size 49: 49: 49: There were 2 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 49: Setting the LD random seed to -56895883 49: 49: Generated 10 of the 10 non-bonded parameter combinations 49: 49: Generated 10 of the 10 1-4 parameter combinations 49: 49: Excluding 0 bonded neighbours molecule type 'A' 49: 49: Setting gen_seed to -537272842 49: 49: Velocities were taken from a Maxwell distribution at 300 K 49: Analysing residue names: 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 49: 49: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 49: 49: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 49: 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: 49: This run will generate roughly 0 Mb of data 49: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (2 ms) 49: [----------] 1 test from GromppDirectiveTest (2 ms total) 49: 49: [----------] 5 tests from InsertMoleculesTest 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 8 atoms)! 49: 49: Added 1 molecules (out of 1 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 49: 49: Output configuration contains 8 atoms in 4 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (28 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 2 atoms)! 49: Try 2 success (now 4 atoms)! 49: Try 3 success (now 6 atoms)! 49: Try 4 success (now 8 atoms)! 49: Try 5 success (now 10 atoms)! 49: 49: Added 5 molecules (out of 5 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 49: 49: Output configuration contains 10 atoms in 10 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 8 atoms)! 49: Try 2 success (now 10 atoms)! 49: 49: Added 2 molecules (out of 2 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 49: 49: Output configuration contains 10 atoms in 4 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (7 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 650 atoms)! 49: Try 2 success (now 652 atoms)! 49: Try 3 success (now 654 atoms)! 49: Try 4 success (now 656 atoms)! 49: 49: Added 4 molecules (out of 4 requested) 49: Replaced 8 residues (24 atoms) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 49: 49: Output configuration contains 632 atoms in 212 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (21 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Read 4 positions from file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 49: 49: Try 1 success (now 2 atoms)! 49: Try 2 success (now 4 atoms)! 49: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 49: Try 13 success (now 6 atoms)! 49: 49: Added 3 molecules (out of 4 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 49: 49: Output configuration contains 6 atoms in 3 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (2 ms) 49: [----------] 5 tests from InsertMoleculesTest (61 ms total) 49: 49: [----------] 3 tests from MassRepartitioning 49: [ RUN ] MassRepartitioning.ValidCaseWorks 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 49: [ RUN ] MassRepartitioning.UnboundGivesWarning 49: 49: WARNING 1 [file unknown]: 49: The are 1 atoms that have a mass below the mass repartitioning limit but 49: are not bound. These masses cannot be repartitioned. 49: 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 49: [ RUN ] MassRepartitioning.LightPartnerGivesError 49: 49: ERROR 1 [file unknown]: 49: Light atoms are bound to at least one atom that has a too low mass for 49: repartioning 49: 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 49: [----------] 3 tests from MassRepartitioning (0 ms total) 49: 49: [----------] 35 tests from GetIrTest 49: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 49: Ignoring obsolete mdp entry 'title' 49: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (15 ms) 49: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 49: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (16 ms) 49: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsKeyWithoutValue (15 ms) 49: [ RUN ] GetIrTest.RejectsValueWithoutKey 49: [ OK ] GetIrTest.RejectsValueWithoutKey (24 ms) 49: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 49: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (31 ms) 49: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (11 ms) 49: [ RUN ] GetIrTest.AcceptsEmptyLines 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsEmptyLines (2 ms) 49: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 49: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 49: [ RUN ] GetIrTest.MtsCheckNstenergy 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (5) 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 49: [ RUN ] GetIrTest.MtsCheckNstpcouple 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 49: Pressure coupling incorrect number of values (I need exactly 1) 49: 49: 49: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 49: Pressure coupling incorrect number of values (I need exactly 1) 49: 49: 49: ERROR 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: With multiple time stepping, nstpcouple should be a multiple of 49: mts-factor 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: 49: ERROR 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: The Berendsen barostat does not generate any strictly correct ensemble, 49: and should not be used for new production simulations (in our opinion). 49: We recommend using the C-rescale barostat instead. 49: 49: 49: ERROR 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: compressibility must be > 0 when using pressure coupling Berendsen 49: 49: 49: [ OK ] GetIrTest.MtsCheckNstpcouple (1 ms) 49: [ RUN ] GetIrTest.MtsCheckNstdhdl 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstdhdl (5) 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: 49: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: Lambda state must be set, either with init-lambda-state or with 49: init-lambda 49: 49: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 49: [ RUN ] GetIrTest.MtsCheckSDNotSupported 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 49: Multiple time stepping is only supported with integrator md 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckSDNotSupported (25 ms) 49: [ RUN ] GetIrTest.AcceptsElectricField 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricField (12 ms) 49: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 49: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (22 ms) 49: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 49: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (13 ms) 49: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsImplicitSolventNo (10 ms) 49: [ RUN ] GetIrTest.RejectsImplicitSolventYes 49: [ OK ] GetIrTest.RejectsImplicitSolventYes (11 ms) 49: [ RUN ] GetIrTest.AcceptsMimic 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsMimic (13 ms) 49: [ RUN ] GetIrTest.AcceptsTransformationCoord 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 49: pull-coord2 has a non-zero force constant and is also referenced in 49: pull-coord1-expression. Make sure that this is intended. In most use 49: cases, the pull coordinates referenced by a transformation coordinate 49: should have their force constant set to zero. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsTransformationCoord (1 ms) 49: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 49: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 49: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 49: pull-coord2 can not use pull-coord1 in the transformation since this is a 49: constraint 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 49: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 49: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 49: 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 49: [ RUN ] GetIrTest.MissingTransformationCoordExpression 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 49: pull-coord1-expression not set for pull coordinate of geometry 49: 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MissingTransformationCoordExpression (13 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (6 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 49: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 49: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 49: in total 100001 steps. This is not compatible with using soft-core 49: potentials. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 49: won't change anymore after step 100000 until the end of the simulation 49: after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (9 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 49: won't change anymore after step 100000 until the end of the simulation 49: after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 49: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 49: components won't change anymore after step 100000 until the end of the 49: simulation after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 49: components won't change anymore after step 100000 until the end of the 49: simulation after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (2 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 49: [----------] 35 tests from GetIrTest (279 ms total) 49: 49: [----------] 6 tests from SolvateTest 49: [ RUN ] SolvateTest.cs_box_Works 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 1x1x1 boxes 49: Solvent box contains 270 atoms in 90 residues 49: Removed 129 solvent atoms due to solvent-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 47 residues 49: Generated solvent containing 141 atoms in 47 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 49: 49: Output configuration contains 141 atoms in 47 residues 49: Volume : 1.331 (nm^3) 49: Density : 1056.36 (g/l) 49: Number of solvent molecules: 47 49: 49: [ OK ] SolvateTest.cs_box_Works (16 ms) 49: [ RUN ] SolvateTest.cs_cp_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 886 residues 49: Generated solvent containing 2658 atoms in 886 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 49: 49: Output configuration contains 2664 atoms in 888 residues 49: Volume : 27.2709 (nm^3) 49: Density : 974.777 (g/l) 49: Number of solvent molecules: 886 49: 49: [ OK ] SolvateTest.cs_cp_Works (32 ms) 49: [ RUN ] SolvateTest.cs_cp_p_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 886 residues 49: Generated solvent containing 2658 atoms in 886 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 49: 49: Output configuration contains 2664 atoms in 888 residues 49: Volume : 27.2709 (nm^3) 49: Density : 974.777 (g/l) 49: Number of solvent molecules: 886 49: 49: Processing topology 49: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 49: [ OK ] SolvateTest.cs_cp_p_Works (29 ms) 49: [ RUN ] SolvateTest.shell_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 1902 solvent atoms more than 1.000000 nm from solute. 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 252 residues 49: Generated solvent containing 756 atoms in 252 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 49: 49: Output configuration contains 762 atoms in 254 residues 49: Volume : 27.2709 (nm^3) 49: Density : 279.3 (g/l) 49: Number of solvent molecules: 252 49: 49: [ OK ] SolvateTest.shell_Works (19 ms) 49: [ RUN ] SolvateTest.update_Topology_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 3x3x3 boxes 49: Solvent box contains 14952 atoms in 4984 residues 49: Removed 2787 solvent atoms due to solvent-solvent overlap 49: Removed 30 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 2 different molecule types: 49: HOH ( 3 atoms): 1876 residues 49: SOL ( 3 atoms): 2169 residues 49: Generated solvent containing 0 atoms in 0 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 49: 49: Output configuration contains 12141 atoms in 4047 residues 49: Volume : 125 (nm^3) 49: Density : 968.963 (g/l) 49: Number of solvent molecules: 4045 49: 49: Processing topology 49: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 49: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 49: [ OK ] SolvateTest.update_Topology_Works (114 ms) 49: [ RUN ] SolvateTest.cs_pdb_big_box_Works 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 1218 atoms in 406 residues 49: Removed 555 solvent atoms due to solvent-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 221 residues 49: Generated solvent containing 663 atoms in 221 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 49: 49: Output configuration contains 663 atoms in 221 residues 49: Volume : 8 (nm^3) 49: Density : 826.409 (g/l) 49: Number of solvent molecules: 221 49: 49: [ OK ] SolvateTest.cs_pdb_big_box_Works (18 ms) 49: [----------] 6 tests from SolvateTest (231 ms total) 49: 49: [----------] 1 test from TopDirTests 49: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 49: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 49: [----------] 1 test from TopDirTests (2 ms total) 49: 49: [----------] 45 tests from SinglePeptideFragments/EditconfTest 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (7 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (13 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (7 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (11 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (4 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (15 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (3 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (6 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (5 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (0 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 49: 49: Select a group for output: 49: Group 0 ( two_residues) has 23 elements 49: There is one group in the index 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (0 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (3 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (12 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (4 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : 0.212 1.187 3.527 (nm) 49: new center : 4.028 2.819 3.723 (nm) 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (6 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.42 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.42 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (11 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.42 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (12 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (11 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (15 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (2 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (13 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: shift : -0.814 1.104 2.657 (nm) 49: new center : 3.002 2.736 2.852 (nm) 49: new box vectors : 6.004 5.472 5.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 187.40 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.28 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.28 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (7 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.28 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (12 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (7 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (1 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (14 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (8 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (15 ms) 49: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 49: Note that major changes are planned in future for editconf, to improve usability and utility. 49: Read 252 atoms 49: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 49: No velocities found 49: system size : 2.004 1.472 1.704 (nm) 49: center : 3.816 1.632 0.195 (nm) 49: box vectors : 8.056 5.637 7.445 (nm) 49: box angles : 90.00 90.00 90.00 (degrees) 49: box volume : 338.10 (nm^3) 49: new center : 3.816 1.632 0.195 (nm) 49: new box vectors : 5.004 4.472 4.704 (nm) 49: new box angles : 90.00 90.00 90.00 (degrees) 49: new box volume : 105.27 (nm^3) 49: 49: WARNING: No boxtype specified - distance condition applied in each dimension. 49: If the molecule rotates the actual distance will be smaller. You might want 49: to use a cubic box instead, or why not try a dodecahedron today? 49: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (12 ms) 49: [----------] 45 tests from SinglePeptideFragments/EditconfTest (315 ms total) 49: 49: [----------] 16 tests from CorrectVelocity/MaxwellTest 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (10 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (10 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (7 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (6 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (6 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (19 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (7 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (7 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 49: [----------] 16 tests from CorrectVelocity/MaxwellTest (83 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 138 tests from 13 test suites ran. (2785 ms total) 49: [ PASSED ] 138 tests. 49/87 Test #49: GmxPreprocessTests ........................ Passed 2.83 sec test 50 Start 50: Pdb2gmx1Test 50: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Pdb2gmx1Test.xml" 50: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests 50: Test timeout computed to be: 1920 50: [==========] Running 30 tests from 1 test suite. 50: [----------] Global test environment set-up. 50: [----------] 30 tests from Oplsaa/Pdb2gmxTest 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (70 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (88 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (49 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (37 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (158 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (49 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (52 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (52 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (52 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (151 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (44 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (91 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (98 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (70 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (285 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (70 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (75 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (71 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (75 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (261 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (104 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (81 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (90 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (66 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (271 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (122 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (113 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (101 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge -0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (102 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (343 ms) 50: [----------] 30 tests from Oplsaa/Pdb2gmxTest (3358 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 30 tests from 1 test suite ran. (3358 ms total) 50: [ PASSED ] 30 tests. 50/87 Test #50: Pdb2gmx1Test .............................. Passed 3.42 sec test 51 Start 51: Pdb2gmx2Test 51: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Pdb2gmx2Test.xml" 51: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 40 tests from 2 test suites. 51: [----------] Global test environment set-up. 51: [----------] 20 tests from G43a1/Pdb2gmxTest 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (116 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (128 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (102 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (114 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (233 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 37 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 37 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (112 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 53 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 51 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (141 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 36 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 36 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (102 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 33 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 31 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (115 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 146 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 137 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (243 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (112 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (133 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (110 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (122 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (239 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 37 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 37 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (86 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 53 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 51 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (101 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 36 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 36 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (98 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 33 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 31 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (83 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 146 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 137 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (205 ms) 51: [----------] 20 tests from G43a1/Pdb2gmxTest (2736 ms total) 51: 51: [----------] 20 tests from G53a6/Pdb2gmxTest 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (101 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (111 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (97 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (134 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (214 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 39 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 39 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (122 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 57 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 55 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (121 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 38 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 38 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (114 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 35 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 33 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (119 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 150 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 141 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (159 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (56 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (65 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (54 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (63 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (108 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 39 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 39 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (47 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 57 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 55 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (58 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 38 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 38 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (37 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 35 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 33 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (36 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 150 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 141 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (126 ms) 51: [----------] 20 tests from G53a6/Pdb2gmxTest (1965 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 40 tests from 2 test suites ran. (4717 ms total) 51: [ PASSED ] 40 tests. 51/87 Test #51: Pdb2gmx2Test .............................. Passed 4.78 sec test 52 Start 52: Pdb2gmx3Test 52: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Pdb2gmx3Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 39 tests from 6 test suites. 52: [----------] Global test environment set-up. 52: [----------] 10 tests from Amber/Pdb2gmxTest 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 653 pairs 52: Before cleaning: 691 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 255, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 691 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.132 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (132 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 748 pairs 52: Before cleaning: 788 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 291, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 788 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.366 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (136 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 676 pairs 52: Before cleaning: 727 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 262, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 727 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.124 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (129 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 603 pairs 52: Before cleaning: 634 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 233, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 634 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.888 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (101 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 2499 pairs 52: Before cleaning: 2631 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 952, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2631 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.576 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (271 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 691 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 255, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 691 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.132 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (81 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 788 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 291, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 788 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.366 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (89 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 727 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 262, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 727 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.124 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (72 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 634 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 233, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 634 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.888 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (46 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2631 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 952, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2631 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.576 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (159 ms) 52: [----------] 10 tests from Amber/Pdb2gmxTest (1229 ms total) 52: 52: [----------] 1 test from AmberTip4p/Pdb2gmxTest 52: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 52: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 2 4 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (4 atoms, 2 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 2 residues with 8 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 4, now 4 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 2 angles 52: 0 pairs, 4 bonds and 0 virtual sites 52: 52: Total mass 36.032 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 52: 52: The Amber99sb-ildn force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (18 ms) 52: [----------] 1 test from AmberTip4p/Pdb2gmxTest (18 ms total) 52: 52: [----------] 12 tests from Charmm/Pdb2gmxTest 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 663 dihedrals, 48 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.115 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (59 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 778 dihedrals, 49 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.361 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (38 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 696 dihedrals, 39 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.130 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (25 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 618 dihedrals, 38 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.885 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (24 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 56 cmap torsion pairs 52: 52: There are 2524 dihedrals, 149 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.566 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (206 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 39 pairs 52: Before cleaning: 39 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 52: Read 'GLU', 9 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 52: 52: chain #res #atoms 52: 52: 1 'X' 1 9 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'X' (9 atoms, 1 residues) 52: 52: Identified residue GLU1 as a starting terminus. 52: 52: Identified residue GLU1 as a ending terminus. 52: Start terminus GLU-1: NH3+ 52: End terminus GLU-1: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 1 residues with 18 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 17, now 17 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 39 dihedrals, 2 impropers, 30 angles 52: 39 pairs, 17 bonds and 0 virtual sites 52: 52: Total mass 146.123 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (46 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 663 dihedrals, 48 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.115 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (113 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 778 dihedrals, 49 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.361 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (93 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 696 dihedrals, 39 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.130 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (78 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 618 dihedrals, 38 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.885 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (83 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 56 cmap torsion pairs 52: 52: There are 2524 dihedrals, 149 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.566 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (210 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 8 virtual sites 52: Added 2 dummy masses 52: Added 3 new constraints 52: Before cleaning: 39 pairs 52: Before cleaning: 39 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 52: Read 'GLU', 9 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 52: 52: chain #res #atoms 52: 52: 1 'X' 1 9 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'X' (9 atoms, 1 residues) 52: 52: Identified residue GLU1 as a starting terminus. 52: 52: Identified residue GLU1 as a ending terminus. 52: Start terminus GLU-1: NH3+ 52: End terminus GLU-1: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 1 residues with 18 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 17, now 17 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 39 dihedrals, 2 impropers, 30 angles 52: 39 pairs, 17 bonds and 9 virtual sites 52: 52: Total mass 146.123 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (42 ms) 52: [----------] 12 tests from Charmm/Pdb2gmxTest (1023 ms total) 52: 52: [----------] 8 tests from ChainSep/Pdb2gmxTest 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 651 pairs 52: Before cleaning: 661 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: Start terminus PHE-6: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 258 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 258, now 258 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 10 cmap torsion pairs 52: 52: There are 661 dihedrals, 46 impropers, 463 angles 52: 648 pairs, 258 bonds and 0 virtual sites 52: 52: Total mass 1882.146 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (142 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 123 pairs 52: Before cleaning: 123 dihedrals 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 10 donors and 7 acceptors were found. 52: There are 7 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS8 52: NE223 52: MET12 SD55 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 317 pairs 52: Before cleaning: 322 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 4 28 52: 52: 2 'B' 7 58 52: 52: 3 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (28 atoms, 4 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 51 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 50, now 50 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 123 dihedrals, 9 impropers, 88 angles 52: 123 pairs, 50 bonds and 0 virtual sites 52: 52: Total mass 434.421 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (58 atoms, 7 residues) 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus PHE-6: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 7 residues with 124 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 125, now 125 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 5 cmap torsion pairs 52: 52: There are 322 dihedrals, 19 impropers, 227 angles 52: 314 pairs, 125 bonds and 0 virtual sites 52: 52: Total mass 846.083 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 51 atoms 4 residues 52: 52: Including chain 2 in system: 124 atoms 7 residues 52: 52: Including chain 3 in system: 83 atoms 5 residues 52: 52: Now there are 258 atoms and 16 residues 52: 52: Total mass in system 1882.146 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (97 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 651 pairs 52: Before cleaning: 661 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ILE-9: COO- 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 258 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 258, now 258 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 10 cmap torsion pairs 52: 52: There are 661 dihedrals, 46 impropers, 463 angles 52: 648 pairs, 258 bonds and 0 virtual sites 52: 52: Total mass 1882.146 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (134 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 10 donors and 12 acceptors were found. 52: There are 13 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 52: SG9 52: HIS8 NE251 1.055 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 288 pairs 52: Before cleaning: 293 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 152 pairs 52: Before cleaning: 152 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 8 61 52: 52: 2 'B' 3 25 52: 52: 3 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (61 atoms, 8 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ILE-9: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 8 residues with 114 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 115, now 115 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6 cmap torsion pairs 52: 52: There are 293 dihedrals, 23 impropers, 203 angles 52: 285 pairs, 115 bonds and 0 virtual sites 52: 52: Total mass 888.952 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (25 atoms, 3 residues) 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 61 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 60, now 60 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 152 dihedrals, 5 impropers, 112 angles 52: 152 pairs, 60 bonds and 0 virtual sites 52: 52: Total mass 391.552 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 114 atoms 8 residues 52: 52: Including chain 2 in system: 61 atoms 3 residues 52: 52: Including chain 3 in system: 83 atoms 5 residues 52: 52: Now there are 258 atoms and 16 residues 52: 52: Total mass in system 1882.146 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (97 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 650 pairs 52: Before cleaning: 660 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Merged chains into joint molecule definitions at 3 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: Start terminus PHE-6: NH3+ 52: End terminus ILE-9: COO- 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 261 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 260, now 260 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 8 cmap torsion pairs 52: 52: There are 660 dihedrals, 45 impropers, 466 angles 52: 647 pairs, 260 bonds and 0 virtual sites 52: 52: Total mass 1900.162 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (130 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 123 pairs 52: Before cleaning: 123 dihedrals 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 6 donors and 4 acceptors were found. 52: There are 3 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 164 pairs 52: Before cleaning: 169 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 152 pairs 52: Before cleaning: 152 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 4 28 52: 52: 2 'B' 4 33 52: 52: 3 'B' 3 25 52: 52: 4 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (28 atoms, 4 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 51 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 50, now 50 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 123 dihedrals, 9 impropers, 88 angles 52: 123 pairs, 50 bonds and 0 virtual sites 52: 52: Total mass 434.421 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (33 atoms, 4 residues) 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: Start terminus PHE-6: NH3+ 52: End terminus ILE-9: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 66 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 67, now 67 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 169 dihedrals, 13 impropers, 118 angles 52: 161 pairs, 67 bonds and 0 virtual sites 52: 52: Total mass 472.547 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'B' (25 atoms, 3 residues) 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 61 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 60, now 60 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 152 dihedrals, 5 impropers, 112 angles 52: 152 pairs, 60 bonds and 0 virtual sites 52: 52: Total mass 391.552 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 4 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 51 atoms 4 residues 52: 52: Including chain 2 in system: 66 atoms 4 residues 52: 52: Including chain 3 in system: 61 atoms 3 residues 52: 52: Including chain 4 in system: 83 atoms 5 residues 52: 52: Now there are 261 atoms and 16 residues 52: 52: Total mass in system 1900.162 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (98 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 652 pairs 52: Before cleaning: 662 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: Merged chains into joint molecule definitions at 1 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 256, now 256 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 12 cmap torsion pairs 52: 52: There are 662 dihedrals, 47 impropers, 460 angles 52: 649 pairs, 256 bonds and 0 virtual sites 52: 52: Total mass 1864.131 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (133 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 14 donors and 15 acceptors were found. 52: There are 20 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 441 pairs 52: Before cleaning: 446 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 11 86 52: 52: 2 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (86 atoms, 11 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 11 residues with 172 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 173, now 173 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 9 cmap torsion pairs 52: 52: There are 446 dihedrals, 29 impropers, 312 angles 52: 438 pairs, 173 bonds and 0 virtual sites 52: 52: Total mass 1262.488 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 172 atoms 11 residues 52: 52: Including chain 2 in system: 83 atoms 5 residues 52: 52: Now there are 255 atoms and 16 residues 52: 52: Total mass in system 1864.131 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (96 ms) 52: [----------] 8 tests from ChainSep/Pdb2gmxTest (931 ms total) 52: 52: [----------] 4 tests from ChainChanges/Pdb2gmxTest 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (52 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (52 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (72 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (68 ms) 52: [----------] 4 tests from ChainChanges/Pdb2gmxTest (246 ms total) 52: 52: [----------] 4 tests from Cyclic/Pdb2gmxTest 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: WARNING: all CONECT records are ignored 52: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 6040 pairs 52: Before cleaning: 6605 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 6040 pairs 52: Before cleaning: 6605 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 52: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: Moved all the water blocks to the end 52: 52: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 52: 52: chain #res #atoms 52: 52: 1 'P' 71 1527 52: 52: 2 'Q' 71 1527 52: 52: 3 'Q' 7 7 52: 52: 4 ' ' 10 10 (only water) 52: 52: 5 ' ' 16 16 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'P' (1527 atoms, 71 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 71 residues with 2297 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 2481, now 2481 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6605 dihedrals, 183 impropers, 4434 angles 52: 5827 pairs, 2481 bonds and 0 virtual sites 52: 52: Total mass 22984.514 a.m.u. 52: 52: Total charge -71.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'Q' (1527 atoms, 71 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 71 residues with 2297 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 2481, now 2481 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6605 dihedrals, 183 impropers, 4434 angles 52: 5827 pairs, 2481 bonds and 0 virtual sites 52: 52: Total mass 22984.514 a.m.u. 52: 52: Total charge -71.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'Q' (7 atoms, 7 residues) 52: 52: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 52: 52: Disabling further notes about ions. 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 7 residues with 7 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: No bonds 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 0 angles 52: 0 pairs, 0 bonds and 0 virtual sites 52: 52: Total mass 170.135 a.m.u. 52: 52: Total charge 14.000 e 52: 52: Writing topology 52: 52: Processing chain 4 (10 atoms, 10 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 10 residues with 30 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 30, now 30 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 30 angles 52: 0 pairs, 30 bonds and 0 virtual sites 52: 52: Total mass 180.154 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Processing chain 5 (16 atoms, 16 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 48 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 48, now 48 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 48 angles 52: 0 pairs, 48 bonds and 0 virtual sites 52: 52: Total mass 288.246 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Including chain 1 in system: 2297 atoms 71 residues 52: 52: Including chain 2 in system: 2297 atoms 71 residues 52: 52: Including chain 3 in system: 7 atoms 7 residues 52: 52: Including chain 4 in system: 30 atoms 10 residues 52: 52: Including chain 5 in system: 48 atoms 16 residues 52: 52: Now there are 4679 atoms and 175 residues 52: 52: Total mass in system 46607.562 a.m.u. 52: 52: Total charge in system -128.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (1011 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2325 pairs 52: Before cleaning: 2325 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 52: Read 'CARNOCYCLIN-A', 413 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 60 413 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (413 atoms, 60 residues) 52: 52: Identified residue LEU1 as a starting terminus. 52: 52: Identified residue LEU60 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 60 residues with 878 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 880, now 880 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 60 cmap torsion pairs 52: 52: There are 2325 dihedrals, 137 impropers, 1614 angles 52: 2319 pairs, 880 bonds and 0 virtual sites 52: 52: Total mass 5866.087 a.m.u. 52: 52: Total charge 4.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (285 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: WARNING: all CONECT records are ignored 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 12080 pairs 52: Before cleaning: 13210 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 52: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Moved all the water blocks to the end 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 52: 52: chain #res #atoms 52: 52: 1 'P' 149 3061 52: 52: 2 ' ' 10 10 (only water) 52: 52: 3 ' ' 16 16 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'P' (3061 atoms, 149 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 52: 52: Disabling further notes about ions. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 149 residues with 4601 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 4962, now 4962 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 13210 dihedrals, 366 impropers, 8868 angles 52: 11654 pairs, 4962 bonds and 0 virtual sites 52: 52: Total mass 46139.162 a.m.u. 52: 52: Total charge -128.000 e 52: 52: Writing topology 52: 52: Processing chain 2 (10 atoms, 10 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 10 residues with 30 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 30, now 30 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 30 angles 52: 0 pairs, 30 bonds and 0 virtual sites 52: 52: Total mass 180.154 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Processing chain 3 (16 atoms, 16 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 48 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 48, now 48 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 48 angles 52: 0 pairs, 48 bonds and 0 virtual sites 52: 52: Total mass 288.246 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Including chain 1 in system: 4601 atoms 149 residues 52: 52: Including chain 2 in system: 30 atoms 10 residues 52: 52: Including chain 3 in system: 48 atoms 16 residues 52: 52: Now there are 4679 atoms and 175 residues 52: 52: Total mass in system 46607.562 a.m.u. 52: 52: Total charge in system -128.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (1631 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2325 pairs 52: Before cleaning: 2325 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 52: Read 'CARNOCYCLIN-A', 413 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 60 413 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (413 atoms, 60 residues) 52: 52: Identified residue LEU1 as a starting terminus. 52: 52: Identified residue LEU60 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 60 residues with 878 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 880, now 880 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 60 cmap torsion pairs 52: 52: There are 2325 dihedrals, 137 impropers, 1614 angles 52: 2319 pairs, 880 bonds and 0 virtual sites 52: 52: Total mass 5866.087 a.m.u. 52: 52: Total charge 4.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (212 ms) 52: [----------] 4 tests from Cyclic/Pdb2gmxTest (3141 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 39 tests from 6 test suites ran. (6590 ms total) 52: [ PASSED ] 39 tests. 52/87 Test #52: Pdb2gmx3Test .............................. Passed 6.67 sec test 53 Start 53: CorrelationsTest 53: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/CorrelationsTest.xml" 53: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/correlationfunctions/tests 53: Test timeout computed to be: 30 53: [==========] Running 21 tests from 3 test suites. 53: [----------] Global test environment set-up. 53: [----------] 10 tests from AutocorrTest 53: [ RUN ] AutocorrTest.EacNormal 53: [ OK ] AutocorrTest.EacNormal (82 ms) 53: [ RUN ] AutocorrTest.EacNoNormalize 53: [ OK ] AutocorrTest.EacNoNormalize (32 ms) 53: [ RUN ] AutocorrTest.EacCos 53: [ OK ] AutocorrTest.EacCos (62 ms) 53: [ RUN ] AutocorrTest.EacVector 53: [ OK ] AutocorrTest.EacVector (57 ms) 53: [ RUN ] AutocorrTest.EacRcross 53: [ OK ] AutocorrTest.EacRcross (0 ms) 53: [ RUN ] AutocorrTest.EacP0 53: [ OK ] AutocorrTest.EacP0 (50 ms) 53: [ RUN ] AutocorrTest.EacP1 53: [ OK ] AutocorrTest.EacP1 (58 ms) 53: [ RUN ] AutocorrTest.EacP2 53: [ OK ] AutocorrTest.EacP2 (124 ms) 53: [ RUN ] AutocorrTest.EacP3 53: [ OK ] AutocorrTest.EacP3 (1 ms) 53: [ RUN ] AutocorrTest.EacP4 53: [ OK ] AutocorrTest.EacP4 (57 ms) 53: [----------] 10 tests from AutocorrTest (529 ms total) 53: 53: [----------] 10 tests from ExpfitTest 53: [ RUN ] ExpfitTest.EffnEXP1 53: [ OK ] ExpfitTest.EffnEXP1 (6 ms) 53: [ RUN ] ExpfitTest.EffnEXP2 53: [ OK ] ExpfitTest.EffnEXP2 (4 ms) 53: [ RUN ] ExpfitTest.EffnEXPEXP 53: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 53: [ RUN ] ExpfitTest.EffnEXP5 53: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 53: [ RUN ] ExpfitTest.EffnEXP7 53: [ OK ] ExpfitTest.EffnEXP7 (21 ms) 53: [ RUN ] ExpfitTest.EffnEXP9 53: [ OK ] ExpfitTest.EffnEXP9 (22 ms) 53: [ RUN ] ExpfitTest.EffnERF 53: [ OK ] ExpfitTest.EffnERF (17 ms) 53: [ RUN ] ExpfitTest.EffnERREST 53: [ OK ] ExpfitTest.EffnERREST (1 ms) 53: [ RUN ] ExpfitTest.EffnVAC 53: [ OK ] ExpfitTest.EffnVAC (27 ms) 53: [ RUN ] ExpfitTest.EffnPRES 53: [ OK ] ExpfitTest.EffnPRES (26 ms) 53: [----------] 10 tests from ExpfitTest (129 ms total) 53: 53: [----------] 1 test from ManyAutocorrelationTest 53: [ RUN ] ManyAutocorrelationTest.Empty 53: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 53: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 21 tests from 3 test suites ran. (662 ms total) 53: [ PASSED ] 21 tests. 53/87 Test #53: CorrelationsTest .......................... Passed 0.77 sec test 54 Start 54: AnalysisDataUnitTests 54: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/analysisdata/tests 54: Test timeout computed to be: 30 54: [==========] Running 69 tests from 14 test suites. 54: [----------] Global test environment set-up. 54: [----------] 3 tests from AnalysisDataInitializationTest 54: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 54: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 54: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 54: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 54: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 54: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 54: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 54: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 54: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (16 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/1 (17 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 54: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 54: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 54: 54: [----------] 4 tests from AnalysisArrayDataTest 54: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 54: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisArrayDataTest.StorageWorks 54: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 54: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 54: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 54: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 54: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 54: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 54: 54: [----------] 6 tests from AverageModuleTest 54: [ RUN ] AverageModuleTest.BasicTest 54: [ OK ] AverageModuleTest.BasicTest (14 ms) 54: [ RUN ] AverageModuleTest.HandlesMultipointData 54: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 54: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 54: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 54: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 54: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 54: [ RUN ] AverageModuleTest.CanCustomizeXAxis 54: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 54: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 54: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 54: [----------] 6 tests from AverageModuleTest (15 ms total) 54: 54: [----------] 2 tests from FrameAverageModuleTest 54: [ RUN ] FrameAverageModuleTest.BasicTest 54: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 54: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 54: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (4 ms) 54: [----------] 2 tests from FrameAverageModuleTest (5 ms total) 54: 54: [----------] 7 tests from AnalysisHistogramSettingsTest 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 54: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 54: 54: [----------] 2 tests from SimpleHistogramModuleTest 54: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 54: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (0 ms) 54: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 54: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [----------] 2 tests from SimpleHistogramModuleTest (0 ms total) 54: 54: [----------] 3 tests from WeightedHistogramModuleTest 54: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 54: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 54: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 54: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 54: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (10 ms) 54: [----------] 3 tests from WeightedHistogramModuleTest (11 ms total) 54: 54: [----------] 3 tests from BinAverageModuleTest 54: [ RUN ] BinAverageModuleTest.ComputesCorrectly 54: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 54: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 54: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 54: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 3 tests from BinAverageModuleTest (1 ms total) 54: 54: [----------] 4 tests from AbstractAverageHistogramTest 54: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 54: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 54: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 54: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 54: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 54: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 54: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 54: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 54: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 54: 54: [----------] 3 tests from LifetimeModuleTest 54: [ RUN ] LifetimeModuleTest.BasicTest 54: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 54: [ RUN ] LifetimeModuleTest.CumulativeTest 54: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 54: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 54: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 3 tests from LifetimeModuleTest (0 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 69 tests from 14 test suites ran. (57 ms total) 54: [ PASSED ] 69 tests. 54/87 Test #54: AnalysisDataUnitTests ..................... Passed 0.14 sec test 55 Start 55: CoordinateIOTests 55: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/CoordinateIOTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/coordinateio/tests 55: Test timeout computed to be: 30 55: [==========] Running 67 tests from 20 test suites. 55: [----------] Global test environment set-up. 55: [----------] 1 test from OutputSelectorDeathTest 55: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (45 ms) 55: [----------] 1 test from OutputSelectorDeathTest (45 ms total) 55: 55: [----------] 5 tests from TrajectoryFrameWriterTest 55: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (10 ms) 55: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 55: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 55: [----------] 5 tests from TrajectoryFrameWriterTest (13 ms total) 55: 55: [----------] 5 tests from OutputAdapterContainer 55: [ RUN ] OutputAdapterContainer.MakeEmpty 55: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 55: [ RUN ] OutputAdapterContainer.AddAdapter 55: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.RejectBadAdapter 55: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 55: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 55: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 55: [----------] 5 tests from OutputAdapterContainer (0 ms total) 55: 55: [----------] 3 tests from RegisterFrameConverterTest 55: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 55: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 55: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 55: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 55: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 55: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 55: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 55: 55: [----------] 5 tests from FlagTest 55: [ RUN ] FlagTest.CanSetSimpleFlag 55: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 55: [ RUN ] FlagTest.CanAddNewBox 55: [ OK ] FlagTest.CanAddNewBox (0 ms) 55: [ RUN ] FlagTest.SetsImplicitPrecisionChange 55: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 55: [ RUN ] FlagTest.SetsImplicitStartTimeChange 55: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 55: [ RUN ] FlagTest.SetsImplicitTimeStepChange 55: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 55: [----------] 5 tests from FlagTest (0 ms total) 55: 55: [----------] 5 tests from SetAtomsTest 55: [ RUN ] SetAtomsTest.RemovesExistingAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 55: [ RUN ] SetAtomsTest.AddsNewAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 55: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (20 ms) 55: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 55: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 55: [----------] 5 tests from SetAtomsTest (24 ms total) 55: 55: [----------] 2 tests from SetBothTimeTest 55: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 55: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 55: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 55: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 55: [----------] 2 tests from SetBothTimeTest (0 ms total) 55: 55: [----------] 2 tests from SetStartTimeTest 55: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 55: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 55: [ RUN ] SetStartTimeTest.WorksWithZeroStart 55: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 55: [----------] 2 tests from SetStartTimeTest (0 ms total) 55: 55: [----------] 1 test from SetTimeStepTest 55: [ RUN ] SetTimeStepTest.SetTimeStepWorks 55: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 55: [----------] 1 test from SetTimeStepTest (0 ms total) 55: 55: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (16 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 55: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (21 ms total) 55: 55: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (24 ms) 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (26 ms total) 55: 55: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 55: 55: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (22 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (1 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (5 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (1 ms) 55: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (32 ms total) 55: 55: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (12 ms) 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (14 ms total) 55: 55: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 55: 55: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 55: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 55: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 55: 55: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 55: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 55: 55: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 55: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (13 ms) 55: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (14 ms total) 55: 55: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 55: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 55: 55: [----------] 4 tests from ModuleSupported/NoOptionalOutput 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (12 ms) 55: [----------] 4 tests from ModuleSupported/NoOptionalOutput (15 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 67 tests from 20 test suites ran. (210 ms total) 55: [ PASSED ] 67 tests. 55/87 Test #55: CoordinateIOTests ......................... Passed 0.26 sec test 56 Start 56: TrajectoryAnalysisUnitTests 56: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests 56: Test timeout computed to be: 1920 56: [==========] Running 385 tests from 24 test suites. 56: [----------] Global test environment set-up. 56: [----------] 11 tests from AngleModuleTest 56: [ RUN ] AngleModuleTest.ComputesSimpleAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesSimpleAngles (15 ms) 56: [ RUN ] AngleModuleTest.ComputesDihedrals 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (18 ms) 56: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (3 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (16 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 56: Reading frames from gro file 'Test system for different angles', 33 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesMultipleAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesMultipleAngles (6 ms) 56: [ RUN ] AngleModuleTest.HandlesDynamicSelections 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms) 56: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (12 ms) 56: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 56: [----------] 11 tests from AngleModuleTest (89 ms total) 56: 56: [----------] 5 tests from ClustsizeTest 56: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 56: There is one group in the index 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 24 56: cmid: 2, cmax: 4, max_size: 6 56: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 56: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (9 ms) 56: [ RUN ] ClustsizeTest.NoMolShortCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 56: There is one group in the index 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 24 56: cmid: 1, cmax: 6, max_size: 6 56: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 56: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (2 ms) 56: [ RUN ] ClustsizeTest.MolDefaultCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 2, cmax: 4, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (5 ms) 56: [ RUN ] ClustsizeTest.MolShortCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 1, cmax: 6, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (0 ms) 56: [ RUN ] ClustsizeTest.MolCSize 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 2, cmax: 4, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolCSize (0 ms) 56: [----------] 5 tests from ClustsizeTest (19 ms total) 56: 56: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 56: Reading frames from gro file 'Test system', 8 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (17 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 56: Reading frames from gro file 'Test system', 8 atoms. 56: Reading frame 0 time 0.000 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 56: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (19 ms total) 56: 56: [----------] 4 tests from ConvertTrjModuleTest 56: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (24 ms) 56: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (33 ms) 56: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (0 ms) 56: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (1 ms) 56: [----------] 4 tests from ConvertTrjModuleTest (60 ms total) 56: 56: [----------] 6 tests from DistanceModuleTest 56: [ RUN ] DistanceModuleTest.ComputesDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2: 56: Number of samples: 5 56: Average distance: 1.43246 nm 56: Standard deviation: 0.96700 nm 56: [ OK ] DistanceModuleTest.ComputesDistances (9 ms) 56: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2: 56: Number of samples: 5 56: Average distance: 1.43246 nm 56: Standard deviation: 0.96700 nm 56: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 56: Number of samples: 4 56: Average distance: 1.81066 nm 56: Standard deviation: 0.79289 nm 56: [ OK ] DistanceModuleTest.ComputesMultipleDistances (8 ms) 56: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2 and res_cog x < 2.8: 56: Number of samples: 3 56: Average distance: 1.72076 nm 56: Standard deviation: 1.24839 nm 56: [ OK ] DistanceModuleTest.HandlesDynamicSelections (7 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: Contacts: 56: Number of samples: 2 56: Average distance: 1.00000 nm 56: Standard deviation: 0.00000 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (40 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: SuccessiveContacts: 56: Number of samples: 2 56: Average distance: 1.00000 nm 56: Standard deviation: 0.00000 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (29 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: ManyContacts: 56: Number of samples: 10 56: Average distance: 1.82913 nm 56: Standard deviation: 0.78478 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (11 ms) 56: [----------] 6 tests from DistanceModuleTest (120 ms total) 56: 56: [----------] 2 tests from ExtractClusterModuleTest 56: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 56: trr version: GMX_trn_file (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 56: Analyzed 26 frames, last time 0.050 56: There are 8 clusters containing 26 structures, highest framenr is 25 56: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (12 ms) 56: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 56: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 56: Analyzed 26 frames, last time 0.050 56: There are 8 clusters containing 26 structures, highest framenr is 25 56: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 56: [----------] 2 tests from ExtractClusterModuleTest (14 ms total) 56: 56: [----------] 2 tests from FreeVolumeModuleTest 56: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for 40 particles. These were set to zero. 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: cutoff = 0.18 nm 56: probe_radius = 0 nm 56: seed = 13 56: ninsert = 1000 probes per nm^3 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 56: van der Spoel and Luciano T. Costa 56: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 56: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 56: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Free volume 38.02 +/- 0.00 % 56: Total volume 68.92 +/- 0.00 nm^3 56: Number of molecules 340 total mass 63491.38 Dalton 56: Average molar mass: 186.74 Dalton 56: Density rho: 1529.71 +/- 0.00 nm^3 56: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 56: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 56: Fractional free volume 0.194 +/- 0.000 56: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (182 ms) 56: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: cutoff = 0.18 nm 56: probe_radius = 0 nm 56: seed = 17 56: ninsert = 1000 probes per nm^3 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 56: van der Spoel and Luciano T. Costa 56: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 56: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 56: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Free volume 38.48 +/- 0.00 % 56: Total volume 68.92 +/- 0.00 nm^3 56: Number of molecules 340 total mass 63491.38 Dalton 56: Average molar mass: 186.74 Dalton 56: Density rho: 1529.71 +/- 0.00 nm^3 56: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 56: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 56: Fractional free volume 0.200 +/- 0.000 56: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (168 ms) 56: [----------] 2 tests from FreeVolumeModuleTest (351 ms total) 56: 56: [----------] 11 tests from MsdModuleTest 56: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.threeDimensionalDiffusion (15 ms) 56: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 56: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.oneDimensionalDiffusion (10 ms) 56: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 56: [ RUN ] MsdModuleTest.roundingFail 56: Reading frame 0 time 0.000 Reading frame 1 time 0.001 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.roundingFail (0 ms) 56: [ RUN ] MsdModuleTest.multipleGroupsWork 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -805571073 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.multipleGroupsWork (82 ms) 56: [ DISABLED ] MsdModuleTest.DISABLED_trestartLessThanDt 56: [ RUN ] MsdModuleTest.trestartGreaterThanDt 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -5252161 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.trestartGreaterThanDt (60 ms) 56: [ RUN ] MsdModuleTest.molTest 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -807404321 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.molTest (51 ms) 56: [ RUN ] MsdModuleTest.beginFit 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to 2144579004 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.beginFit (47 ms) 56: [ RUN ] MsdModuleTest.endFit 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -512819395 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.endFit (41 ms) 56: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: NOTE: You provided an index file 56: /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 56: (with -n), but it was not used by any selection. 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to 1404862407 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (34 ms) 56: [----------] 11 tests from MsdModuleTest (346 ms total) 56: 56: [----------] 9 tests from PairDistanceModuleTest 56: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (10 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (6 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (6 ms) 56: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 56: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (2 ms) 56: [----------] 9 tests from PairDistanceModuleTest (33 ms total) 56: 56: [----------] 5 tests from RdfModuleTest 56: [ RUN ] RdfModuleTest.BasicTest 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.BasicTest (52 ms) 56: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 56: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (54 ms) 56: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (53 ms) 56: [ RUN ] RdfModuleTest.CalculatesSurf 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.CalculatesSurf (34 ms) 56: [ RUN ] RdfModuleTest.CalculatesXY 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.CalculatesXY (64 ms) 56: [----------] 5 tests from RdfModuleTest (259 ms total) 56: 56: [----------] 5 tests from SasaModuleTest 56: [ RUN ] SasaModuleTest.BasicTest 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.BasicTest (44 ms) 56: [ RUN ] SasaModuleTest.HandlesSelectedResidues 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesSelectedResidues (21 ms) 56: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (10 ms) 56: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (21 ms) 56: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (7 ms) 56: [----------] 5 tests from SasaModuleTest (118 ms total) 56: 56: [----------] 8 tests from SelectModuleTest 56: [ RUN ] SelectModuleTest.BasicTest 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.BasicTest (30 ms) 56: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (7 ms) 56: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (15 ms) 56: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 56: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 56: [ RUN ] SelectModuleTest.NormalizesSizes 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.NormalizesSizes (20 ms) 56: [ RUN ] SelectModuleTest.WritesResidueNumbers 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 56: [ RUN ] SelectModuleTest.WritesResidueIndices 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.WritesResidueIndices (14 ms) 56: [----------] 8 tests from SelectModuleTest (93 ms total) 56: 56: [----------] 10 tests from SurfaceAreaTest 56: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 56: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 56: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 56: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 56: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 56: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints12 56: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints32 56: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints42 56: [ OK ] SurfaceAreaTest.SurfacePoints42 (5 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints122 56: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 56: [ RUN ] SurfaceAreaTest.Computes100Points 56: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 56: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 56: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 56: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 56: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (15 ms) 56: [----------] 10 tests from SurfaceAreaTest (24 ms total) 56: 56: [----------] 4 tests from TopologyInformation 56: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 56: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 56: [ RUN ] TopologyInformation.WorksWithGroFile 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 56: [ RUN ] TopologyInformation.WorksWithPdbFile 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 56: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file lysozyme.top, line 1465]: 56: System has non-zero total charge: 2.000000 56: Total charge should normally be an integer. See 56: https://manual.gromacs.org/current/user-guide/floating-point.html 56: for discussion on how close it should be to an integer. 56: 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 465.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: NVE simulation with an initial temperature of zero: will use a Verlet 56: buffer of 10%. Check your energy drift! 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 4 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 56: Setting the LD random seed to -84025928 56: 56: Generated 330891 of the 330891 non-bonded parameter combinations 56: 56: Generated 330891 of the 330891 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 56: Analysing residue names: 56: There are: 10 Protein residues 56: Analysing Protein... 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (849 ms) 56: [----------] 4 tests from TopologyInformation (851 ms total) 56: 56: [----------] 4 tests from TrajectoryModuleTest 56: [ RUN ] TrajectoryModuleTest.BasicTest 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.BasicTest (1 ms) 56: [ RUN ] TrajectoryModuleTest.PlotsXOnly 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.PlotsXOnly (21 ms) 56: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 56: [ RUN ] TrajectoryModuleTest.HandlesNoForces 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.HandlesNoForces (2 ms) 56: [----------] 4 tests from TrajectoryModuleTest (27 ms total) 56: 56: [----------] 5 tests from UnionFinderTest 56: [ RUN ] UnionFinderTest.WorksEmpty 56: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 56: [ RUN ] UnionFinderTest.BasicMerges 56: [ OK ] UnionFinderTest.BasicMerges (0 ms) 56: [ RUN ] UnionFinderTest.LargerMerges 56: [ OK ] UnionFinderTest.LargerMerges (0 ms) 56: [ RUN ] UnionFinderTest.LongRightMerge 56: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 56: [ RUN ] UnionFinderTest.LongLeftMerge 56: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 56: [----------] 5 tests from UnionFinderTest (0 ms total) 56: 56: [----------] 1 test from MappedUnionFinderTest 56: [ RUN ] MappedUnionFinderTest.BasicMerges 56: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 56: [----------] 1 test from MappedUnionFinderTest (0 ms total) 56: 56: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/0 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/0 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/1 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/1 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/2 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/2 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/3 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/3 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/4 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/4 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/5 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/5 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/6 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/6 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/7 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/7 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/8 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/8 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/9 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/9 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/10 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/10 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/11 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/11 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/12 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/12 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/13 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/13 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/14 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/14 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/15 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/15 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/16 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/16 (52 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/17 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/17 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/18 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/18 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/19 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/19 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/20 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/20 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/21 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/21 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/22 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/22 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/23 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/23 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/24 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/24 (75 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/25 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/25 (52 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/26 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/26 (62 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/27 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/27 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/28 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/28 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/29 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/29 (78 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/30 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/30 (86 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/31 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/31 (65 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/32 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/32 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/33 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/33 (6 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/34 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/34 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/35 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/35 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/36 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/36 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/37 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/37 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/38 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/38 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/39 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/39 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/40 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/40 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/41 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/41 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/42 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/42 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/43 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/43 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/44 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/44 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/45 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/45 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/46 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/46 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/47 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/47 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/48 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/48 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/49 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/49 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/50 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/50 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/51 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/51 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/52 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/52 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/53 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/53 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/54 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/54 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/55 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/55 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/56 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/56 (54 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/57 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/57 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/58 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/58 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/59 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/59 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/60 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/60 (49 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/61 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/61 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/62 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/62 (56 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/63 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/63 (95 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/64 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/64 (54 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/65 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/65 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/66 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/66 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/67 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/67 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/68 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/68 (71 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/69 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/69 (62 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/70 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/70 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/71 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/71 (63 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/72 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/72 (47 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/73 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/73 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/74 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/74 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/75 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/75 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/76 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/76 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/77 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/77 (50 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/78 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/78 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/79 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/79 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/80 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/80 (86 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/81 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/81 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/82 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/82 (52 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/83 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/83 (66 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/84 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/84 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/85 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/85 (66 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/86 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/86 (61 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/87 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/87 (82 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/88 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/88 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/89 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/89 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/90 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/90 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/91 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/91 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/92 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/92 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/93 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/93 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/94 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/94 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/95 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/95 (48 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/96 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/96 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/97 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/97 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/98 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/98 (50 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/99 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/99 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/100 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/100 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/101 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/101 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/102 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/102 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/103 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/103 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/104 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/104 (48 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/105 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/105 (54 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/106 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/106 (50 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/107 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/107 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/108 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/108 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/109 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/109 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/110 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/110 (54 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/111 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/111 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/112 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/112 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/113 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/113 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/114 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/114 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/115 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/115 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/116 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/116 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/117 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/117 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/118 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/118 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/119 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/119 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/120 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/120 (214 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/121 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/121 (128 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/122 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/122 (129 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/123 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/123 (177 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/124 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/124 (189 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/125 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/125 (206 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/126 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/126 (188 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/127 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/127 (189 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/128 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/128 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/129 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/129 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/130 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/130 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/131 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/131 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/132 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/132 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/133 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/133 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/134 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/134 (56 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/135 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/135 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/136 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/136 (65 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/137 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/137 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/138 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/138 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/139 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/139 (62 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/140 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/140 (54 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/141 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/141 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/142 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/142 (62 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/143 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/143 (54 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/144 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/144 (56 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/145 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/145 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/146 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/146 (61 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/147 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/147 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/148 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/148 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/149 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/149 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/150 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/150 (62 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/151 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/151 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/152 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/152 (83 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/153 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/153 (79 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/154 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/154 (79 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/155 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/155 (75 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/156 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/156 (80 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/157 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/157 (76 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/158 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/158 (96 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/159 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/159 (76 ms) 56: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB (8391 ms total) 56: 56: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 (177 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 (151 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 (155 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 (152 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 (153 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 (160 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 (184 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 (160 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 (61 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 (58 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 (62 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 (47 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 (44 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 (44 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 (56 ms) 56: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB (2099 ms total) 56: 56: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 (77 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 (98 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 (64 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 (71 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 (72 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 (68 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 (72 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 (67 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 (93 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 (125 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 (109 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 (121 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 (52 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 (52 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 (86 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 (106 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 (89 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 (101 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 (74 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 (82 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 (86 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 (87 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 (75 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 (73 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 (89 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 (68 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 (47 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 (135 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 (142 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 (146 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 (171 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 (48 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 (44 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 (46 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 (40 ms) 56: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB (4541 ms total) 56: 56: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 (78 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 (90 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 (80 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 (103 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 (46 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 (28 ms) 56: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB (640 ms total) 56: 56: [----------] 3 tests from GyrateTests/GyrateModuleTest 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (26 ms) 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (12 ms) 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (16 ms) 56: [----------] 3 tests from GyrateTests/GyrateModuleTest (55 ms total) 56: 56: [----------] 6 tests from HBondTests/HbondModuleTest 56: [ RUN ] HBondTests/HbondModuleTest.Works/0 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/0 (23 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/1 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/1 (33 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/2 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/2 (242 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/3 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 56: Merging hbonds with Acceptor and Donor swapped 56: [ OK ] HBondTests/HbondModuleTest.Works/3 (225 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/4 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/4 (231 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/5 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/5 (214 ms) 56: [----------] 6 tests from HBondTests/HbondModuleTest (1050 ms total) 56: 56: [----------] 4 tests from MoleculeTests/ScatteringModule 56: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (49 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: D. T. Cromer & J. B. Mann 56: X-ray scattering factors computed from numerical Hartree-Fock wave functions 56: Acta Cryst. A 24 (1968) pp. 321 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (809 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (17 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: D. T. Cromer & J. B. Mann 56: X-ray scattering factors computed from numerical Hartree-Fock wave functions 56: Acta Cryst. A 24 (1968) pp. 321 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (190 ms) 56: [----------] 4 tests from MoleculeTests/ScatteringModule (1085 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 385 tests from 24 test suites ran. (20295 ms total) 56: [ PASSED ] 385 tests. 56: 56: YOU HAVE 1 DISABLED TEST 56: 56/87 Test #56: TrajectoryAnalysisUnitTests ............... Passed 20.40 sec test 57 Start 57: EnergyAnalysisUnitTests 57: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests 57: Test timeout computed to be: 30 57: [==========] Running 11 tests from 5 test suites. 57: [----------] Global test environment set-up. 57: [----------] 2 tests from EnergyTermTest 57: [ RUN ] EnergyTermTest.ConstructWorks 57: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 57: [ RUN ] EnergyTermTest.AddFrameWorks 57: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 57: [----------] 2 tests from EnergyTermTest (0 ms total) 57: 57: [----------] 1 test from DhdlTest 57: [ RUN ] DhdlTest.ExtractDhdl 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 57: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 57: Note: file tpx version 110, software tpx version 134 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 57: 57: 57: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 57: [ OK ] DhdlTest.ExtractDhdl (47 ms) 57: [----------] 1 test from DhdlTest (47 ms total) 57: 57: [----------] 1 test from OriresTest 57: [ RUN ] OriresTest.ExtractOrires 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 57: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 57: Note: file tpx version 111, software tpx version 134 57: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 57: End your selection with 0 57: Selecting all 7 orientation restraints 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 57: [ OK ] OriresTest.ExtractOrires (40 ms) 57: [----------] 1 test from OriresTest (40 ms total) 57: 57: [----------] 5 tests from EnergyTest 57: [ RUN ] EnergyTest.ExtractEnergy 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 57: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 57: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 57: [ OK ] EnergyTest.ExtractEnergy (1 ms) 57: [ RUN ] EnergyTest.ExtractEnergyByNumber 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 57: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 57: Pres. DC -268.49 3 8.52175 13.2804 (bar) 57: [ OK ] EnergyTest.ExtractEnergyByNumber (13 ms) 57: [ RUN ] EnergyTest.ExtractEnergyMixed 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 57: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 57: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 57: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 57: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 57: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 57: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 57: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 57: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 57: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 57: 37 1/Viscosity 38 T-System 39 Lamb-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 57: 57: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 57: All statistics are over 3 points (frames) 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 57: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 57: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 57: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 57: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 57: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 57: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 57: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 57: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 57: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 57: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 57: 37 1/Viscosity 38 T-System 39 Lamb-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 57: 57: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 57: All statistics are over 3 points (frames) 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 57: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 57: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 57: [----------] 5 tests from EnergyTest (17 ms total) 57: 57: [----------] 2 tests from ViscosityTest 57: [ RUN ] ViscosityTest.EinsteinViscosity 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Pres-XX 20.2092 65 717.193 185.978 (bar) 57: Pres-XY -47.7351 39 372.522 207.456 (bar) 57: Pres-XZ 11.477 31 379.79 6.80818 (bar) 57: Pres-YX -47.7106 39 372.525 207.5 (bar) 57: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 57: Pres-YZ -41.3534 45 401.216 114.663 (bar) 57: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 57: Pres-ZY -41.3119 45 401.196 114.743 (bar) 57: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 57: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: 57: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 57: [ OK ] ViscosityTest.EinsteinViscosity (168 ms) 57: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Pres-XX 20.2092 65 717.193 185.978 (bar) 57: Pres-XY -47.7351 39 372.522 207.456 (bar) 57: Pres-XZ 11.477 31 379.79 6.80818 (bar) 57: Pres-YX -47.7106 39 372.525 207.5 (bar) 57: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 57: Pres-YZ -41.3534 45 401.216 114.663 (bar) 57: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 57: Pres-ZY -41.3119 45 401.196 114.743 (bar) 57: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 57: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: 57: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 57: [ OK ] ViscosityTest.EinsteinViscosityIntegral (100 ms) 57: [----------] 2 tests from ViscosityTest (269 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 11 tests from 5 test suites ran. (375 ms total) 57: [ PASSED ] 11 tests. 57/87 Test #57: EnergyAnalysisUnitTests ................... Passed 0.44 sec test 58 Start 58: ToolUnitTests 58: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/ToolUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests 58: Test timeout computed to be: 1920 58: [==========] Running 62 tests from 7 test suites. 58: [----------] Global test environment set-up. 58: [----------] 2 tests from DumpTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Setting the LD random seed to 1072430263 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ RUN ] DumpTest.WorksWithTpr 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 58: inputrec: 58: integrator = md 58: tinit = 0 58: dt = 0.001 58: nsteps = 0 58: init-step = 0 58: simulation-part = 1 58: mts = false 58: mass-repartition-factor = 1 58: comm-mode = Linear 58: nstcomm = 100 58: bd-fric = 0 58: ld-seed = 1072430263 58: emtol = 10 58: emstep = 0.01 58: niter = 20 58: fcstep = 0 58: nstcgsteep = 1000 58: nbfgscorr = 10 58: rtpi = 0.05 58: nstxout = 0 58: nstvout = 0 58: nstfout = 0 58: nstlog = 1000 58: nstcalcenergy = 100 58: nstenergy = 1000 58: nstxout-compressed = 0 58: compressed-x-precision = 1000 58: cutoff-scheme = Verlet 58: nstlist = 10 58: pbc = xyz 58: periodic-molecules = false 58: verlet-buffer-tolerance = -1 58: verlet-buffer-pressure-tolerance = 0.5 58: rlist = 1.1 58: coulombtype = Cut-off 58: coulomb-modifier = Potential-shift 58: rcoulomb-switch = 0 58: rcoulomb = 1 58: epsilon-r = 1 58: epsilon-rf = inf 58: vdw-type = Cut-off 58: vdw-modifier = Potential-shift 58: rvdw-switch = 0 58: rvdw = 1 58: DispCorr = No 58: table-extension = 1 58: fourierspacing = 0.12 58: fourier-nx = 0 58: fourier-ny = 0 58: fourier-nz = 0 58: pme-order = 4 58: ewald-rtol = 1e-05 58: ewald-rtol-lj = 0.001 58: lj-pme-comb-rule = Geometric 58: ewald-geometry = 3d 58: epsilon-surface = 0 58: ensemble-temperature-setting = not available 58: tcoupl = No 58: nsttcouple = -1 58: nh-chain-length = 0 58: print-nose-hoover-chain-variables = false 58: pcoupl = No 58: refcoord-scaling = No 58: posres-com (3): 58: posres-com[0]= 0.00000e+00 58: posres-com[1]= 0.00000e+00 58: posres-com[2]= 0.00000e+00 58: posres-comB (3): 58: posres-comB[0]= 0.00000e+00 58: posres-comB[1]= 0.00000e+00 58: posres-comB[2]= 0.00000e+00 58: QMMM = false 58: qm-opts: 58: ngQM = 0 58: constraint-algorithm = Lincs 58: continuation = false 58: Shake-SOR = false 58: shake-tol = 0.0001 58: lincs-order = 4 58: lincs-iter = 1 58: lincs-warnangle = 30 58: nwall = 0 58: wall-type = 9-3 58: wall-r-linpot = -1 58: wall-atomtype[0] = -1 58: wall-atomtype[1] = -1 58: wall-density[0] = 0 58: wall-density[1] = 0 58: wall-ewald-zfac = 3 58: pull = false 58: awh = false 58: rotation = false 58: interactiveMD = false 58: disre = No 58: disre-weighting = Conservative 58: disre-mixed = false 58: dr-fc = 1000 58: dr-tau = 0 58: nstdisreout = 100 58: orire-fc = 0 58: orire-tau = 0 58: nstorireout = 100 58: free-energy = no 58: cos-acceleration = 0 58: deform (3x3): 58: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: simulated-tempering = false 58: swapcoords = no 58: userint1 = 0 58: userint2 = 0 58: userint3 = 0 58: userint4 = 0 58: userreal1 = 0 58: userreal2 = 0 58: userreal3 = 0 58: userreal4 = 0 58: applied-forces: 58: electric-field: 58: x: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: y: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: z: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: density-guided-simulation: 58: active = false 58: group = protein 58: similarity-measure = inner-product 58: atom-spreading-weight = unity 58: force-constant = 1e+09 58: gaussian-transform-spreading-width = 0.2 58: gaussian-transform-spreading-range-in-multiples-of-width = 4 58: reference-density-filename = reference.mrc 58: nst = 1 58: normalize-densities = true 58: adaptive-force-scaling = false 58: adaptive-force-scaling-time-constant = 4 58: shift-vector = 58: transformation-matrix = 58: qmmm-cp2k: 58: active = false 58: qmgroup = System 58: qmmethod = PBE 58: qmfilenames = 58: qmcharge = 0 58: qmmultiplicity = 1 58: colvars: 58: active = false 58: configfile = 58: seed = -1 58: grpopts: 58: nrdf: 465 58: ref-t: 0 58: tau-t: 0 58: annealing: No 58: annealing-npoints: 0 58: acc: 0 0 0 58: nfreeze: N N N 58: energygrp-flags[ 0]: 0 58: header: 58: bIr = present 58: bBox = present 58: bTop = present 58: bX = present 58: bV = present 58: bF = not present 58: natoms = 156 58: lambda = 0.000000e+00 58: buffer size = 46180 58: topology: 58: name="First 10 residues from 1AKI" 58: #atoms = 156 58: #molblock = 1 58: molblock (0): 58: moltype = 0 "Protein_chain_B" 58: #molecules = 1 58: #posres_xA = 0 58: #posres_xB = 0 58: bIntermolecularInteractions = false 58: ffparams: 58: atnr=10 58: ntypes=212 58: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 58: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 58: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 58: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 58: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 58: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 58: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 58: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 58: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 58: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 58: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 58: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 58: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 58: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 58: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 58: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 58: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 58: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 58: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 58: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 58: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 58: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 58: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 58: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 58: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 58: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 58: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 58: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 58: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 58: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 58: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 58: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 58: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 58: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 58: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 58: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 58: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 58: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 58: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 58: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 58: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 58: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 58: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 58: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 58: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 58: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 58: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 58: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 58: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 58: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 58: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 58: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 58: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 58: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 58: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 58: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 58: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 58: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 58: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 58: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 58: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 58: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 58: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 58: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 58: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 58: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 58: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 58: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 58: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 58: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 58: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 58: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 58: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 58: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 58: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 58: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 58: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 58: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 58: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 58: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 58: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 58: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 58: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 58: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 58: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 58: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 58: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 58: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 58: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 58: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 58: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 58: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 58: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 58: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 58: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 58: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 58: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 58: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 58: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 58: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 58: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 58: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 58: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 58: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 58: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 58: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 58: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 58: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 58: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 58: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 58: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 58: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 58: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 58: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 58: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 58: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 58: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 58: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 58: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 58: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 58: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 58: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 58: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 58: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 58: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 58: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 58: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 58: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 58: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 58: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 58: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 58: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 58: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 58: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 58: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 58: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 58: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 58: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 58: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 58: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 58: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 58: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 58: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 58: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 58: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 58: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 58: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 58: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 58: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 58: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 58: reppow = 12 58: fudgeQQ = 0.5 58: cmap 58: moltype (0): 58: name="Protein_chain_B" 58: atoms: 58: atom (156): 58: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 58: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 58: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 58: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 58: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 58: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 58: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 58: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 58: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 58: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 58: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 58: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 58: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 58: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 58: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 58: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 58: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 58: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 58: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 58: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 58: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 58: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 58: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 58: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 58: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 58: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 58: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 58: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 58: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 58: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 58: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 58: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 58: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 58: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 58: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 58: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 58: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 58: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 58: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 58: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 58: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 58: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 58: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 58: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 58: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 58: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 58: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 58: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 58: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 58: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 58: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 58: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 58: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 58: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 58: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 58: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 58: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 58: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 58: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 58: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 58: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 58: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 58: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 58: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 58: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 58: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 58: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 58: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 58: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 58: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 58: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 58: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 58: atom (156): 58: atom[0]={name="N"} 58: atom[1]={name="H1"} 58: atom[2]={name="H2"} 58: atom[3]={name="H3"} 58: atom[4]={name="CA"} 58: atom[5]={name="HA"} 58: atom[6]={name="CB"} 58: atom[7]={name="HB1"} 58: atom[8]={name="HB2"} 58: atom[9]={name="CG"} 58: atom[10]={name="HG1"} 58: atom[11]={name="HG2"} 58: atom[12]={name="CD"} 58: atom[13]={name="HD1"} 58: atom[14]={name="HD2"} 58: atom[15]={name="CE"} 58: atom[16]={name="HE1"} 58: atom[17]={name="HE2"} 58: atom[18]={name="NZ"} 58: atom[19]={name="HZ1"} 58: atom[20]={name="HZ2"} 58: atom[21]={name="HZ3"} 58: atom[22]={name="C"} 58: atom[23]={name="O"} 58: atom[24]={name="N"} 58: atom[25]={name="H"} 58: atom[26]={name="CA"} 58: atom[27]={name="HA"} 58: atom[28]={name="CB"} 58: atom[29]={name="HB"} 58: atom[30]={name="CG1"} 58: atom[31]={name="HG11"} 58: atom[32]={name="HG12"} 58: atom[33]={name="HG13"} 58: atom[34]={name="CG2"} 58: atom[35]={name="HG21"} 58: atom[36]={name="HG22"} 58: atom[37]={name="HG23"} 58: atom[38]={name="C"} 58: atom[39]={name="O"} 58: atom[40]={name="N"} 58: atom[41]={name="H"} 58: atom[42]={name="CA"} 58: atom[43]={name="HA"} 58: atom[44]={name="CB"} 58: atom[45]={name="HB1"} 58: atom[46]={name="HB2"} 58: atom[47]={name="CG"} 58: atom[48]={name="CD1"} 58: atom[49]={name="HD1"} 58: atom[50]={name="CD2"} 58: atom[51]={name="HD2"} 58: atom[52]={name="CE1"} 58: atom[53]={name="HE1"} 58: atom[54]={name="CE2"} 58: atom[55]={name="HE2"} 58: atom[56]={name="CZ"} 58: atom[57]={name="HZ"} 58: atom[58]={name="C"} 58: atom[59]={name="O"} 58: atom[60]={name="N"} 58: atom[61]={name="H"} 58: atom[62]={name="CA"} 58: atom[63]={name="HA1"} 58: atom[64]={name="HA2"} 58: atom[65]={name="C"} 58: atom[66]={name="O"} 58: atom[67]={name="N"} 58: atom[68]={name="H"} 58: atom[69]={name="CA"} 58: atom[70]={name="HA"} 58: atom[71]={name="CB"} 58: atom[72]={name="HB1"} 58: atom[73]={name="HB2"} 58: atom[74]={name="CG"} 58: atom[75]={name="HG1"} 58: atom[76]={name="HG2"} 58: atom[77]={name="CD"} 58: atom[78]={name="HD1"} 58: atom[79]={name="HD2"} 58: atom[80]={name="NE"} 58: atom[81]={name="HE"} 58: atom[82]={name="CZ"} 58: atom[83]={name="NH1"} 58: atom[84]={name="HH11"} 58: atom[85]={name="HH12"} 58: atom[86]={name="NH2"} 58: atom[87]={name="HH21"} 58: atom[88]={name="HH22"} 58: atom[89]={name="C"} 58: atom[90]={name="O"} 58: atom[91]={name="N"} 58: atom[92]={name="H"} 58: atom[93]={name="CA"} 58: atom[94]={name="HA"} 58: atom[95]={name="CB"} 58: atom[96]={name="HB1"} 58: atom[97]={name="HB2"} 58: atom[98]={name="SG"} 58: atom[99]={name="HG"} 58: atom[100]={name="C"} 58: atom[101]={name="O"} 58: atom[102]={name="N"} 58: atom[103]={name="H"} 58: atom[104]={name="CA"} 58: atom[105]={name="HA"} 58: atom[106]={name="CB"} 58: atom[107]={name="HB1"} 58: atom[108]={name="HB2"} 58: atom[109]={name="CG"} 58: atom[110]={name="HG1"} 58: atom[111]={name="HG2"} 58: atom[112]={name="CD"} 58: atom[113]={name="OE1"} 58: atom[114]={name="OE2"} 58: atom[115]={name="C"} 58: atom[116]={name="O"} 58: atom[117]={name="N"} 58: atom[118]={name="H"} 58: atom[119]={name="CA"} 58: atom[120]={name="HA"} 58: atom[121]={name="CB"} 58: atom[122]={name="HB1"} 58: atom[123]={name="HB2"} 58: atom[124]={name="CG"} 58: atom[125]={name="HG"} 58: atom[126]={name="CD1"} 58: atom[127]={name="HD11"} 58: atom[128]={name="HD12"} 58: atom[129]={name="HD13"} 58: atom[130]={name="CD2"} 58: atom[131]={name="HD21"} 58: atom[132]={name="HD22"} 58: atom[133]={name="HD23"} 58: atom[134]={name="C"} 58: atom[135]={name="O"} 58: atom[136]={name="N"} 58: atom[137]={name="H"} 58: atom[138]={name="CA"} 58: atom[139]={name="HA"} 58: atom[140]={name="CB"} 58: atom[141]={name="HB1"} 58: atom[142]={name="HB2"} 58: atom[143]={name="HB3"} 58: atom[144]={name="C"} 58: atom[145]={name="O"} 58: atom[146]={name="N"} 58: atom[147]={name="H"} 58: atom[148]={name="CA"} 58: atom[149]={name="HA"} 58: atom[150]={name="CB"} 58: atom[151]={name="HB1"} 58: atom[152]={name="HB2"} 58: atom[153]={name="HB3"} 58: atom[154]={name="C"} 58: atom[155]={name="O"} 58: type (156): 58: type[0]={name="opls_287",nameB="opls_287"} 58: type[1]={name="opls_290",nameB="opls_290"} 58: type[2]={name="opls_290",nameB="opls_290"} 58: type[3]={name="opls_290",nameB="opls_290"} 58: type[4]={name="opls_293B",nameB="opls_293B"} 58: type[5]={name="opls_140",nameB="opls_140"} 58: type[6]={name="opls_136",nameB="opls_136"} 58: type[7]={name="opls_140",nameB="opls_140"} 58: type[8]={name="opls_140",nameB="opls_140"} 58: type[9]={name="opls_136",nameB="opls_136"} 58: type[10]={name="opls_140",nameB="opls_140"} 58: type[11]={name="opls_140",nameB="opls_140"} 58: type[12]={name="opls_136",nameB="opls_136"} 58: type[13]={name="opls_140",nameB="opls_140"} 58: type[14]={name="opls_140",nameB="opls_140"} 58: type[15]={name="opls_292",nameB="opls_292"} 58: type[16]={name="opls_140",nameB="opls_140"} 58: type[17]={name="opls_140",nameB="opls_140"} 58: type[18]={name="opls_287",nameB="opls_287"} 58: type[19]={name="opls_290",nameB="opls_290"} 58: type[20]={name="opls_290",nameB="opls_290"} 58: type[21]={name="opls_290",nameB="opls_290"} 58: type[22]={name="opls_235",nameB="opls_235"} 58: type[23]={name="opls_236",nameB="opls_236"} 58: type[24]={name="opls_238",nameB="opls_238"} 58: type[25]={name="opls_241",nameB="opls_241"} 58: type[26]={name="opls_224B",nameB="opls_224B"} 58: type[27]={name="opls_140",nameB="opls_140"} 58: type[28]={name="opls_137",nameB="opls_137"} 58: type[29]={name="opls_140",nameB="opls_140"} 58: type[30]={name="opls_135",nameB="opls_135"} 58: type[31]={name="opls_140",nameB="opls_140"} 58: type[32]={name="opls_140",nameB="opls_140"} 58: type[33]={name="opls_140",nameB="opls_140"} 58: type[34]={name="opls_135",nameB="opls_135"} 58: type[35]={name="opls_140",nameB="opls_140"} 58: type[36]={name="opls_140",nameB="opls_140"} 58: type[37]={name="opls_140",nameB="opls_140"} 58: type[38]={name="opls_235",nameB="opls_235"} 58: type[39]={name="opls_236",nameB="opls_236"} 58: type[40]={name="opls_238",nameB="opls_238"} 58: type[41]={name="opls_241",nameB="opls_241"} 58: type[42]={name="opls_224B",nameB="opls_224B"} 58: type[43]={name="opls_140",nameB="opls_140"} 58: type[44]={name="opls_149",nameB="opls_149"} 58: type[45]={name="opls_140",nameB="opls_140"} 58: type[46]={name="opls_140",nameB="opls_140"} 58: type[47]={name="opls_145",nameB="opls_145"} 58: type[48]={name="opls_145",nameB="opls_145"} 58: type[49]={name="opls_146",nameB="opls_146"} 58: type[50]={name="opls_145",nameB="opls_145"} 58: type[51]={name="opls_146",nameB="opls_146"} 58: type[52]={name="opls_145",nameB="opls_145"} 58: type[53]={name="opls_146",nameB="opls_146"} 58: type[54]={name="opls_145",nameB="opls_145"} 58: type[55]={name="opls_146",nameB="opls_146"} 58: type[56]={name="opls_145",nameB="opls_145"} 58: type[57]={name="opls_146",nameB="opls_146"} 58: type[58]={name="opls_235",nameB="opls_235"} 58: type[59]={name="opls_236",nameB="opls_236"} 58: type[60]={name="opls_238",nameB="opls_238"} 58: type[61]={name="opls_241",nameB="opls_241"} 58: type[62]={name="opls_223B",nameB="opls_223B"} 58: type[63]={name="opls_140",nameB="opls_140"} 58: type[64]={name="opls_140",nameB="opls_140"} 58: type[65]={name="opls_235",nameB="opls_235"} 58: type[66]={name="opls_236",nameB="opls_236"} 58: type[67]={name="opls_238",nameB="opls_238"} 58: type[68]={name="opls_241",nameB="opls_241"} 58: type[69]={name="opls_224B",nameB="opls_224B"} 58: type[70]={name="opls_140",nameB="opls_140"} 58: type[71]={name="opls_136",nameB="opls_136"} 58: type[72]={name="opls_140",nameB="opls_140"} 58: type[73]={name="opls_140",nameB="opls_140"} 58: type[74]={name="opls_308",nameB="opls_308"} 58: type[75]={name="opls_140",nameB="opls_140"} 58: type[76]={name="opls_140",nameB="opls_140"} 58: type[77]={name="opls_307",nameB="opls_307"} 58: type[78]={name="opls_140",nameB="opls_140"} 58: type[79]={name="opls_140",nameB="opls_140"} 58: type[80]={name="opls_303",nameB="opls_303"} 58: type[81]={name="opls_304",nameB="opls_304"} 58: type[82]={name="opls_302",nameB="opls_302"} 58: type[83]={name="opls_300",nameB="opls_300"} 58: type[84]={name="opls_301",nameB="opls_301"} 58: type[85]={name="opls_301",nameB="opls_301"} 58: type[86]={name="opls_300",nameB="opls_300"} 58: type[87]={name="opls_301",nameB="opls_301"} 58: type[88]={name="opls_301",nameB="opls_301"} 58: type[89]={name="opls_235",nameB="opls_235"} 58: type[90]={name="opls_236",nameB="opls_236"} 58: type[91]={name="opls_238",nameB="opls_238"} 58: type[92]={name="opls_241",nameB="opls_241"} 58: type[93]={name="opls_224B",nameB="opls_224B"} 58: type[94]={name="opls_140",nameB="opls_140"} 58: type[95]={name="opls_206",nameB="opls_206"} 58: type[96]={name="opls_140",nameB="opls_140"} 58: type[97]={name="opls_140",nameB="opls_140"} 58: type[98]={name="opls_200",nameB="opls_200"} 58: type[99]={name="opls_204",nameB="opls_204"} 58: type[100]={name="opls_235",nameB="opls_235"} 58: type[101]={name="opls_236",nameB="opls_236"} 58: type[102]={name="opls_238",nameB="opls_238"} 58: type[103]={name="opls_241",nameB="opls_241"} 58: type[104]={name="opls_224B",nameB="opls_224B"} 58: type[105]={name="opls_140",nameB="opls_140"} 58: type[106]={name="opls_136",nameB="opls_136"} 58: type[107]={name="opls_140",nameB="opls_140"} 58: type[108]={name="opls_140",nameB="opls_140"} 58: type[109]={name="opls_274",nameB="opls_274"} 58: type[110]={name="opls_140",nameB="opls_140"} 58: type[111]={name="opls_140",nameB="opls_140"} 58: type[112]={name="opls_271",nameB="opls_271"} 58: type[113]={name="opls_272",nameB="opls_272"} 58: type[114]={name="opls_272",nameB="opls_272"} 58: type[115]={name="opls_235",nameB="opls_235"} 58: type[116]={name="opls_236",nameB="opls_236"} 58: type[117]={name="opls_238",nameB="opls_238"} 58: type[118]={name="opls_241",nameB="opls_241"} 58: type[119]={name="opls_224B",nameB="opls_224B"} 58: type[120]={name="opls_140",nameB="opls_140"} 58: type[121]={name="opls_136",nameB="opls_136"} 58: type[122]={name="opls_140",nameB="opls_140"} 58: type[123]={name="opls_140",nameB="opls_140"} 58: type[124]={name="opls_137",nameB="opls_137"} 58: type[125]={name="opls_140",nameB="opls_140"} 58: type[126]={name="opls_135",nameB="opls_135"} 58: type[127]={name="opls_140",nameB="opls_140"} 58: type[128]={name="opls_140",nameB="opls_140"} 58: type[129]={name="opls_140",nameB="opls_140"} 58: type[130]={name="opls_135",nameB="opls_135"} 58: type[131]={name="opls_140",nameB="opls_140"} 58: type[132]={name="opls_140",nameB="opls_140"} 58: type[133]={name="opls_140",nameB="opls_140"} 58: type[134]={name="opls_235",nameB="opls_235"} 58: type[135]={name="opls_236",nameB="opls_236"} 58: type[136]={name="opls_238",nameB="opls_238"} 58: type[137]={name="opls_241",nameB="opls_241"} 58: type[138]={name="opls_224B",nameB="opls_224B"} 58: type[139]={name="opls_140",nameB="opls_140"} 58: type[140]={name="opls_135",nameB="opls_135"} 58: type[141]={name="opls_140",nameB="opls_140"} 58: type[142]={name="opls_140",nameB="opls_140"} 58: type[143]={name="opls_140",nameB="opls_140"} 58: type[144]={name="opls_235",nameB="opls_235"} 58: type[145]={name="opls_236",nameB="opls_236"} 58: type[146]={name="opls_238",nameB="opls_238"} 58: type[147]={name="opls_241",nameB="opls_241"} 58: type[148]={name="opls_224B",nameB="opls_224B"} 58: type[149]={name="opls_140",nameB="opls_140"} 58: type[150]={name="opls_135",nameB="opls_135"} 58: type[151]={name="opls_140",nameB="opls_140"} 58: type[152]={name="opls_140",nameB="opls_140"} 58: type[153]={name="opls_140",nameB="opls_140"} 58: type[154]={name="opls_235",nameB="opls_235"} 58: type[155]={name="opls_236",nameB="opls_236"} 58: residue (10): 58: residue[0]={name="LYS", nr=1, ic=' '} 58: residue[1]={name="VAL", nr=2, ic=' '} 58: residue[2]={name="PHE", nr=3, ic=' '} 58: residue[3]={name="GLY", nr=4, ic=' '} 58: residue[4]={name="ARG", nr=5, ic=' '} 58: residue[5]={name="CYS", nr=6, ic=' '} 58: residue[6]={name="GLU", nr=7, ic=' '} 58: residue[7]={name="LEU", nr=8, ic=' '} 58: residue[8]={name="ALA", nr=9, ic=' '} 58: residue[9]={name="ALA", nr=10, ic=' '} 58: excls: 58: numLists=156 58: numElements=1828 58: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 58: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 58: 23, 24, 25, 26} 58: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 58: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 58: 14, 15, 22, 23, 24} 58: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 58: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 58: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 58: 16, 17, 18, 22} 58: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 58: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 58: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 58: 17, 18, 19, 20, 21} 58: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 58: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 58: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 58: 20, 21} 58: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 58: 26, 27, 28, 38} 58: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 58: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 58: 30, 34, 38, 39, 40} 58: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 58: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 58: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 58: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 58: 40} 58: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 58: 34, 35, 36, 37, 38, 39, 40} 58: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 58: 40, 41, 42, 43, 44, 58} 58: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 58: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 58: 45, 46, 47, 58, 59, 60} 58: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 58: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58: 48, 50, 58, 59, 60, 61, 62} 58: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 58: 60} 58: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 58: 50, 51, 52, 54, 58, 59, 60} 58: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 58: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 58: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 58: 52, 53, 54, 55, 56, 58} 58: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58: 54, 56, 57} 58: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 58: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 58: 55, 56, 57} 58: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 58: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 58: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 58: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 58: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 58: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 58: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 58: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 58: 60, 61, 62, 63, 64, 65} 58: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 58: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 58: 65, 66, 67} 58: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 58: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 58: 68, 69} 58: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 58: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 58: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 58: 70, 71, 89} 58: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 58: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 58: 72, 73, 74, 89, 90, 91} 58: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 58: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 58: 75, 76, 77, 89, 90, 91, 92, 93} 58: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 58: 91} 58: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 58: 77, 78, 79, 80, 89, 90, 91} 58: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 58: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 58: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 58: 79, 80, 81, 82, 89} 58: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 58: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 58: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 58: 81, 82, 83, 86} 58: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 58: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 58: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 58: 84, 85, 86, 87, 88} 58: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 58: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 58: 87, 88} 58: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 58: excls[84][num=6]={80, 82, 83, 84, 85, 86} 58: excls[85][num=6]={80, 82, 83, 84, 85, 86} 58: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 58: excls[87][num=6]={80, 82, 83, 86, 87, 88} 58: excls[88][num=6]={80, 82, 83, 86, 87, 88} 58: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 58: 91, 92, 93, 94, 95, 100} 58: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 58: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 58: 96, 97, 98, 100, 101, 102} 58: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 58: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 58: 99, 100, 101, 102, 103, 104} 58: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 58: 102} 58: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 58: 101, 102} 58: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[99][num=6]={93, 95, 96, 97, 98, 99} 58: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 58: 102, 103, 104, 105, 106, 115} 58: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 58: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 58: 106, 107, 108, 109, 115, 116, 117} 58: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 58: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 58: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 58: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 115, 116, 117} 58: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 110, 111, 112, 113, 114, 115, 116, 117} 58: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 115} 58: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 115} 58: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 113, 114, 115} 58: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 58: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 58: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 115, 116, 117, 118, 119, 120, 121, 134} 58: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 58: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 58: 120, 121, 122, 123, 124, 134, 135, 136} 58: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 58: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 58: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 58: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 134, 135, 136} 58: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 58: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 130, 134} 58: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 130, 134} 58: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 127, 128, 129, 130, 131, 132, 133, 134} 58: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 134, 135, 136, 137, 138, 139, 140, 144} 58: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 58: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 58: 139, 140, 141, 142, 143, 144, 145, 146} 58: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 58: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 58: 142, 143, 144, 145, 146, 147, 148} 58: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146} 58: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146} 58: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146, 147, 148, 149, 150, 154} 58: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 58: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 58: 149, 150, 151, 152, 153, 154, 155} 58: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 58: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 58: 152, 153, 154, 155} 58: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[155][num=6]={146, 148, 149, 150, 154, 155} 58: Bond: 58: nr: 468 58: iatoms: 58: 0 type=100 (BONDS) 0 1 58: 1 type=100 (BONDS) 0 2 58: 2 type=100 (BONDS) 0 3 58: 3 type=101 (BONDS) 0 4 58: 4 type=102 (BONDS) 4 5 58: 5 type=103 (BONDS) 4 6 58: 6 type=104 (BONDS) 4 22 58: 7 type=102 (BONDS) 6 7 58: 8 type=102 (BONDS) 6 8 58: 9 type=103 (BONDS) 6 9 58: 10 type=102 (BONDS) 9 10 58: 11 type=102 (BONDS) 9 11 58: 12 type=103 (BONDS) 9 12 58: 13 type=102 (BONDS) 12 13 58: 14 type=102 (BONDS) 12 14 58: 15 type=103 (BONDS) 12 15 58: 16 type=102 (BONDS) 15 16 58: 17 type=102 (BONDS) 15 17 58: 18 type=101 (BONDS) 15 18 58: 19 type=100 (BONDS) 18 19 58: 20 type=100 (BONDS) 18 20 58: 21 type=100 (BONDS) 18 21 58: 22 type=105 (BONDS) 22 23 58: 23 type=106 (BONDS) 22 24 58: 24 type=100 (BONDS) 24 25 58: 25 type=107 (BONDS) 24 26 58: 26 type=102 (BONDS) 26 27 58: 27 type=103 (BONDS) 26 28 58: 28 type=104 (BONDS) 26 38 58: 29 type=102 (BONDS) 28 29 58: 30 type=103 (BONDS) 28 30 58: 31 type=103 (BONDS) 28 34 58: 32 type=102 (BONDS) 30 31 58: 33 type=102 (BONDS) 30 32 58: 34 type=102 (BONDS) 30 33 58: 35 type=102 (BONDS) 34 35 58: 36 type=102 (BONDS) 34 36 58: 37 type=102 (BONDS) 34 37 58: 38 type=105 (BONDS) 38 39 58: 39 type=106 (BONDS) 38 40 58: 40 type=100 (BONDS) 40 41 58: 41 type=107 (BONDS) 40 42 58: 42 type=102 (BONDS) 42 43 58: 43 type=103 (BONDS) 42 44 58: 44 type=104 (BONDS) 42 58 58: 45 type=102 (BONDS) 44 45 58: 46 type=102 (BONDS) 44 46 58: 47 type=108 (BONDS) 44 47 58: 48 type=109 (BONDS) 47 48 58: 49 type=109 (BONDS) 47 50 58: 50 type=110 (BONDS) 48 49 58: 51 type=109 (BONDS) 48 52 58: 52 type=110 (BONDS) 50 51 58: 53 type=109 (BONDS) 50 54 58: 54 type=110 (BONDS) 52 53 58: 55 type=109 (BONDS) 52 56 58: 56 type=110 (BONDS) 54 55 58: 57 type=109 (BONDS) 54 56 58: 58 type=110 (BONDS) 56 57 58: 59 type=105 (BONDS) 58 59 58: 60 type=106 (BONDS) 58 60 58: 61 type=100 (BONDS) 60 61 58: 62 type=107 (BONDS) 60 62 58: 63 type=102 (BONDS) 62 63 58: 64 type=102 (BONDS) 62 64 58: 65 type=104 (BONDS) 62 65 58: 66 type=105 (BONDS) 65 66 58: 67 type=106 (BONDS) 65 67 58: 68 type=100 (BONDS) 67 68 58: 69 type=107 (BONDS) 67 69 58: 70 type=102 (BONDS) 69 70 58: 71 type=103 (BONDS) 69 71 58: 72 type=104 (BONDS) 69 89 58: 73 type=102 (BONDS) 71 72 58: 74 type=102 (BONDS) 71 73 58: 75 type=103 (BONDS) 71 74 58: 76 type=102 (BONDS) 74 75 58: 77 type=102 (BONDS) 74 76 58: 78 type=103 (BONDS) 74 77 58: 79 type=102 (BONDS) 77 78 58: 80 type=102 (BONDS) 77 79 58: 81 type=111 (BONDS) 77 80 58: 82 type=100 (BONDS) 80 81 58: 83 type=112 (BONDS) 80 82 58: 84 type=112 (BONDS) 82 83 58: 85 type=112 (BONDS) 82 86 58: 86 type=100 (BONDS) 83 84 58: 87 type=100 (BONDS) 83 85 58: 88 type=100 (BONDS) 86 87 58: 89 type=100 (BONDS) 86 88 58: 90 type=105 (BONDS) 89 90 58: 91 type=106 (BONDS) 89 91 58: 92 type=100 (BONDS) 91 92 58: 93 type=107 (BONDS) 91 93 58: 94 type=102 (BONDS) 93 94 58: 95 type=103 (BONDS) 93 95 58: 96 type=104 (BONDS) 93 100 58: 97 type=102 (BONDS) 95 96 58: 98 type=102 (BONDS) 95 97 58: 99 type=113 (BONDS) 95 98 58: 100 type=114 (BONDS) 98 99 58: 101 type=105 (BONDS) 100 101 58: 102 type=106 (BONDS) 100 102 58: 103 type=100 (BONDS) 102 103 58: 104 type=107 (BONDS) 102 104 58: 105 type=102 (BONDS) 104 105 58: 106 type=103 (BONDS) 104 106 58: 107 type=104 (BONDS) 104 115 58: 108 type=102 (BONDS) 106 107 58: 109 type=102 (BONDS) 106 108 58: 110 type=103 (BONDS) 106 109 58: 111 type=102 (BONDS) 109 110 58: 112 type=102 (BONDS) 109 111 58: 113 type=104 (BONDS) 109 112 58: 114 type=115 (BONDS) 112 113 58: 115 type=115 (BONDS) 112 114 58: 116 type=105 (BONDS) 115 116 58: 117 type=106 (BONDS) 115 117 58: 118 type=100 (BONDS) 117 118 58: 119 type=107 (BONDS) 117 119 58: 120 type=102 (BONDS) 119 120 58: 121 type=103 (BONDS) 119 121 58: 122 type=104 (BONDS) 119 134 58: 123 type=102 (BONDS) 121 122 58: 124 type=102 (BONDS) 121 123 58: 125 type=103 (BONDS) 121 124 58: 126 type=102 (BONDS) 124 125 58: 127 type=103 (BONDS) 124 126 58: 128 type=103 (BONDS) 124 130 58: 129 type=102 (BONDS) 126 127 58: 130 type=102 (BONDS) 126 128 58: 131 type=102 (BONDS) 126 129 58: 132 type=102 (BONDS) 130 131 58: 133 type=102 (BONDS) 130 132 58: 134 type=102 (BONDS) 130 133 58: 135 type=105 (BONDS) 134 135 58: 136 type=106 (BONDS) 134 136 58: 137 type=100 (BONDS) 136 137 58: 138 type=107 (BONDS) 136 138 58: 139 type=102 (BONDS) 138 139 58: 140 type=103 (BONDS) 138 140 58: 141 type=104 (BONDS) 138 144 58: 142 type=102 (BONDS) 140 141 58: 143 type=102 (BONDS) 140 142 58: 144 type=102 (BONDS) 140 143 58: 145 type=105 (BONDS) 144 145 58: 146 type=106 (BONDS) 144 146 58: 147 type=100 (BONDS) 146 147 58: 148 type=107 (BONDS) 146 148 58: 149 type=102 (BONDS) 148 149 58: 150 type=103 (BONDS) 148 150 58: 151 type=104 (BONDS) 148 154 58: 152 type=102 (BONDS) 150 151 58: 153 type=102 (BONDS) 150 152 58: 154 type=102 (BONDS) 150 153 58: 155 type=105 (BONDS) 154 155 58: G96Bond: 58: nr: 0 58: Morse: 58: nr: 0 58: Cubic Bonds: 58: nr: 0 58: Connect Bonds: 58: nr: 0 58: Harmonic Pot.: 58: nr: 0 58: FENE Bonds: 58: nr: 0 58: Tab. Bonds: 58: nr: 0 58: Tab. Bonds NC: 58: nr: 0 58: Restraint Pot.: 58: nr: 0 58: Angle: 58: nr: 1124 58: iatoms: 58: 0 type=116 (ANGLES) 1 0 2 58: 1 type=116 (ANGLES) 1 0 3 58: 2 type=116 (ANGLES) 1 0 4 58: 3 type=116 (ANGLES) 2 0 3 58: 4 type=116 (ANGLES) 2 0 4 58: 5 type=116 (ANGLES) 3 0 4 58: 6 type=116 (ANGLES) 0 4 5 58: 7 type=117 (ANGLES) 0 4 6 58: 8 type=117 (ANGLES) 0 4 22 58: 9 type=118 (ANGLES) 5 4 6 58: 10 type=116 (ANGLES) 5 4 22 58: 11 type=119 (ANGLES) 6 4 22 58: 12 type=118 (ANGLES) 4 6 7 58: 13 type=118 (ANGLES) 4 6 8 58: 14 type=120 (ANGLES) 4 6 9 58: 15 type=121 (ANGLES) 7 6 8 58: 16 type=118 (ANGLES) 7 6 9 58: 17 type=118 (ANGLES) 8 6 9 58: 18 type=118 (ANGLES) 6 9 10 58: 19 type=118 (ANGLES) 6 9 11 58: 20 type=120 (ANGLES) 6 9 12 58: 21 type=121 (ANGLES) 10 9 11 58: 22 type=118 (ANGLES) 10 9 12 58: 23 type=118 (ANGLES) 11 9 12 58: 24 type=118 (ANGLES) 9 12 13 58: 25 type=118 (ANGLES) 9 12 14 58: 26 type=120 (ANGLES) 9 12 15 58: 27 type=121 (ANGLES) 13 12 14 58: 28 type=118 (ANGLES) 13 12 15 58: 29 type=118 (ANGLES) 14 12 15 58: 30 type=118 (ANGLES) 12 15 16 58: 31 type=118 (ANGLES) 12 15 17 58: 32 type=117 (ANGLES) 12 15 18 58: 33 type=121 (ANGLES) 16 15 17 58: 34 type=116 (ANGLES) 16 15 18 58: 35 type=116 (ANGLES) 17 15 18 58: 36 type=116 (ANGLES) 15 18 19 58: 37 type=116 (ANGLES) 15 18 20 58: 38 type=116 (ANGLES) 15 18 21 58: 39 type=116 (ANGLES) 19 18 20 58: 40 type=116 (ANGLES) 19 18 21 58: 41 type=116 (ANGLES) 20 18 21 58: 42 type=122 (ANGLES) 4 22 23 58: 43 type=123 (ANGLES) 4 22 24 58: 44 type=124 (ANGLES) 23 22 24 58: 45 type=125 (ANGLES) 22 24 25 58: 46 type=126 (ANGLES) 22 24 26 58: 47 type=127 (ANGLES) 25 24 26 58: 48 type=116 (ANGLES) 24 26 27 58: 49 type=128 (ANGLES) 24 26 28 58: 50 type=129 (ANGLES) 24 26 38 58: 51 type=118 (ANGLES) 27 26 28 58: 52 type=116 (ANGLES) 27 26 38 58: 53 type=119 (ANGLES) 28 26 38 58: 54 type=118 (ANGLES) 26 28 29 58: 55 type=120 (ANGLES) 26 28 30 58: 56 type=120 (ANGLES) 26 28 34 58: 57 type=118 (ANGLES) 29 28 30 58: 58 type=118 (ANGLES) 29 28 34 58: 59 type=120 (ANGLES) 30 28 34 58: 60 type=118 (ANGLES) 28 30 31 58: 61 type=118 (ANGLES) 28 30 32 58: 62 type=118 (ANGLES) 28 30 33 58: 63 type=121 (ANGLES) 31 30 32 58: 64 type=121 (ANGLES) 31 30 33 58: 65 type=121 (ANGLES) 32 30 33 58: 66 type=118 (ANGLES) 28 34 35 58: 67 type=118 (ANGLES) 28 34 36 58: 68 type=118 (ANGLES) 28 34 37 58: 69 type=121 (ANGLES) 35 34 36 58: 70 type=121 (ANGLES) 35 34 37 58: 71 type=121 (ANGLES) 36 34 37 58: 72 type=122 (ANGLES) 26 38 39 58: 73 type=123 (ANGLES) 26 38 40 58: 74 type=124 (ANGLES) 39 38 40 58: 75 type=125 (ANGLES) 38 40 41 58: 76 type=126 (ANGLES) 38 40 42 58: 77 type=127 (ANGLES) 41 40 42 58: 78 type=116 (ANGLES) 40 42 43 58: 79 type=128 (ANGLES) 40 42 44 58: 80 type=129 (ANGLES) 40 42 58 58: 81 type=118 (ANGLES) 43 42 44 58: 82 type=116 (ANGLES) 43 42 58 58: 83 type=119 (ANGLES) 44 42 58 58: 84 type=118 (ANGLES) 42 44 45 58: 85 type=118 (ANGLES) 42 44 46 58: 86 type=130 (ANGLES) 42 44 47 58: 87 type=121 (ANGLES) 45 44 46 58: 88 type=116 (ANGLES) 45 44 47 58: 89 type=116 (ANGLES) 46 44 47 58: 90 type=131 (ANGLES) 44 47 48 58: 91 type=131 (ANGLES) 44 47 50 58: 92 type=132 (ANGLES) 48 47 50 58: 93 type=133 (ANGLES) 47 48 49 58: 94 type=132 (ANGLES) 47 48 52 58: 95 type=133 (ANGLES) 49 48 52 58: 96 type=133 (ANGLES) 47 50 51 58: 97 type=132 (ANGLES) 47 50 54 58: 98 type=133 (ANGLES) 51 50 54 58: 99 type=133 (ANGLES) 48 52 53 58: 100 type=132 (ANGLES) 48 52 56 58: 101 type=133 (ANGLES) 53 52 56 58: 102 type=133 (ANGLES) 50 54 55 58: 103 type=132 (ANGLES) 50 54 56 58: 104 type=133 (ANGLES) 55 54 56 58: 105 type=132 (ANGLES) 52 56 54 58: 106 type=133 (ANGLES) 52 56 57 58: 107 type=133 (ANGLES) 54 56 57 58: 108 type=122 (ANGLES) 42 58 59 58: 109 type=123 (ANGLES) 42 58 60 58: 110 type=124 (ANGLES) 59 58 60 58: 111 type=125 (ANGLES) 58 60 61 58: 112 type=126 (ANGLES) 58 60 62 58: 113 type=127 (ANGLES) 61 60 62 58: 114 type=116 (ANGLES) 60 62 63 58: 115 type=116 (ANGLES) 60 62 64 58: 116 type=129 (ANGLES) 60 62 65 58: 117 type=121 (ANGLES) 63 62 64 58: 118 type=116 (ANGLES) 63 62 65 58: 119 type=116 (ANGLES) 64 62 65 58: 120 type=122 (ANGLES) 62 65 66 58: 121 type=123 (ANGLES) 62 65 67 58: 122 type=124 (ANGLES) 66 65 67 58: 123 type=125 (ANGLES) 65 67 68 58: 124 type=126 (ANGLES) 65 67 69 58: 125 type=127 (ANGLES) 68 67 69 58: 126 type=116 (ANGLES) 67 69 70 58: 127 type=128 (ANGLES) 67 69 71 58: 128 type=129 (ANGLES) 67 69 89 58: 129 type=118 (ANGLES) 70 69 71 58: 130 type=116 (ANGLES) 70 69 89 58: 131 type=119 (ANGLES) 71 69 89 58: 132 type=118 (ANGLES) 69 71 72 58: 133 type=118 (ANGLES) 69 71 73 58: 134 type=120 (ANGLES) 69 71 74 58: 135 type=121 (ANGLES) 72 71 73 58: 136 type=118 (ANGLES) 72 71 74 58: 137 type=118 (ANGLES) 73 71 74 58: 138 type=118 (ANGLES) 71 74 75 58: 139 type=118 (ANGLES) 71 74 76 58: 140 type=120 (ANGLES) 71 74 77 58: 141 type=121 (ANGLES) 75 74 76 58: 142 type=118 (ANGLES) 75 74 77 58: 143 type=118 (ANGLES) 76 74 77 58: 144 type=118 (ANGLES) 74 77 78 58: 145 type=118 (ANGLES) 74 77 79 58: 146 type=117 (ANGLES) 74 77 80 58: 147 type=121 (ANGLES) 78 77 79 58: 148 type=116 (ANGLES) 78 77 80 58: 149 type=116 (ANGLES) 79 77 80 58: 150 type=134 (ANGLES) 77 80 81 58: 151 type=135 (ANGLES) 77 80 82 58: 152 type=133 (ANGLES) 81 80 82 58: 153 type=131 (ANGLES) 80 82 83 58: 154 type=131 (ANGLES) 80 82 86 58: 155 type=131 (ANGLES) 83 82 86 58: 156 type=133 (ANGLES) 82 83 84 58: 157 type=133 (ANGLES) 82 83 85 58: 158 type=133 (ANGLES) 84 83 85 58: 159 type=133 (ANGLES) 82 86 87 58: 160 type=133 (ANGLES) 82 86 88 58: 161 type=133 (ANGLES) 87 86 88 58: 162 type=122 (ANGLES) 69 89 90 58: 163 type=123 (ANGLES) 69 89 91 58: 164 type=124 (ANGLES) 90 89 91 58: 165 type=125 (ANGLES) 89 91 92 58: 166 type=126 (ANGLES) 89 91 93 58: 167 type=127 (ANGLES) 92 91 93 58: 168 type=116 (ANGLES) 91 93 94 58: 169 type=128 (ANGLES) 91 93 95 58: 170 type=129 (ANGLES) 91 93 100 58: 171 type=118 (ANGLES) 94 93 95 58: 172 type=116 (ANGLES) 94 93 100 58: 173 type=119 (ANGLES) 95 93 100 58: 174 type=118 (ANGLES) 93 95 96 58: 175 type=118 (ANGLES) 93 95 97 58: 176 type=136 (ANGLES) 93 95 98 58: 177 type=121 (ANGLES) 96 95 97 58: 178 type=116 (ANGLES) 96 95 98 58: 179 type=116 (ANGLES) 97 95 98 58: 180 type=137 (ANGLES) 95 98 99 58: 181 type=122 (ANGLES) 93 100 101 58: 182 type=123 (ANGLES) 93 100 102 58: 183 type=124 (ANGLES) 101 100 102 58: 184 type=125 (ANGLES) 100 102 103 58: 185 type=126 (ANGLES) 100 102 104 58: 186 type=127 (ANGLES) 103 102 104 58: 187 type=116 (ANGLES) 102 104 105 58: 188 type=128 (ANGLES) 102 104 106 58: 189 type=129 (ANGLES) 102 104 115 58: 190 type=118 (ANGLES) 105 104 106 58: 191 type=116 (ANGLES) 105 104 115 58: 192 type=119 (ANGLES) 106 104 115 58: 193 type=118 (ANGLES) 104 106 107 58: 194 type=118 (ANGLES) 104 106 108 58: 195 type=120 (ANGLES) 104 106 109 58: 196 type=121 (ANGLES) 107 106 108 58: 197 type=118 (ANGLES) 107 106 109 58: 198 type=118 (ANGLES) 108 106 109 58: 199 type=118 (ANGLES) 106 109 110 58: 200 type=118 (ANGLES) 106 109 111 58: 201 type=119 (ANGLES) 106 109 112 58: 202 type=121 (ANGLES) 110 109 111 58: 203 type=116 (ANGLES) 110 109 112 58: 204 type=116 (ANGLES) 111 109 112 58: 205 type=138 (ANGLES) 109 112 113 58: 206 type=138 (ANGLES) 109 112 114 58: 207 type=139 (ANGLES) 113 112 114 58: 208 type=122 (ANGLES) 104 115 116 58: 209 type=123 (ANGLES) 104 115 117 58: 210 type=124 (ANGLES) 116 115 117 58: 211 type=125 (ANGLES) 115 117 118 58: 212 type=126 (ANGLES) 115 117 119 58: 213 type=127 (ANGLES) 118 117 119 58: 214 type=116 (ANGLES) 117 119 120 58: 215 type=128 (ANGLES) 117 119 121 58: 216 type=129 (ANGLES) 117 119 134 58: 217 type=118 (ANGLES) 120 119 121 58: 218 type=116 (ANGLES) 120 119 134 58: 219 type=119 (ANGLES) 121 119 134 58: 220 type=118 (ANGLES) 119 121 122 58: 221 type=118 (ANGLES) 119 121 123 58: 222 type=120 (ANGLES) 119 121 124 58: 223 type=121 (ANGLES) 122 121 123 58: 224 type=118 (ANGLES) 122 121 124 58: 225 type=118 (ANGLES) 123 121 124 58: 226 type=118 (ANGLES) 121 124 125 58: 227 type=120 (ANGLES) 121 124 126 58: 228 type=120 (ANGLES) 121 124 130 58: 229 type=118 (ANGLES) 125 124 126 58: 230 type=118 (ANGLES) 125 124 130 58: 231 type=120 (ANGLES) 126 124 130 58: 232 type=118 (ANGLES) 124 126 127 58: 233 type=118 (ANGLES) 124 126 128 58: 234 type=118 (ANGLES) 124 126 129 58: 235 type=121 (ANGLES) 127 126 128 58: 236 type=121 (ANGLES) 127 126 129 58: 237 type=121 (ANGLES) 128 126 129 58: 238 type=118 (ANGLES) 124 130 131 58: 239 type=118 (ANGLES) 124 130 132 58: 240 type=118 (ANGLES) 124 130 133 58: 241 type=121 (ANGLES) 131 130 132 58: 242 type=121 (ANGLES) 131 130 133 58: 243 type=121 (ANGLES) 132 130 133 58: 244 type=122 (ANGLES) 119 134 135 58: 245 type=123 (ANGLES) 119 134 136 58: 246 type=124 (ANGLES) 135 134 136 58: 247 type=125 (ANGLES) 134 136 137 58: 248 type=126 (ANGLES) 134 136 138 58: 249 type=127 (ANGLES) 137 136 138 58: 250 type=116 (ANGLES) 136 138 139 58: 251 type=128 (ANGLES) 136 138 140 58: 252 type=129 (ANGLES) 136 138 144 58: 253 type=118 (ANGLES) 139 138 140 58: 254 type=116 (ANGLES) 139 138 144 58: 255 type=119 (ANGLES) 140 138 144 58: 256 type=118 (ANGLES) 138 140 141 58: 257 type=118 (ANGLES) 138 140 142 58: 258 type=118 (ANGLES) 138 140 143 58: 259 type=121 (ANGLES) 141 140 142 58: 260 type=121 (ANGLES) 141 140 143 58: 261 type=121 (ANGLES) 142 140 143 58: 262 type=122 (ANGLES) 138 144 145 58: 263 type=123 (ANGLES) 138 144 146 58: 264 type=124 (ANGLES) 145 144 146 58: 265 type=125 (ANGLES) 144 146 147 58: 266 type=126 (ANGLES) 144 146 148 58: 267 type=127 (ANGLES) 147 146 148 58: 268 type=116 (ANGLES) 146 148 149 58: 269 type=128 (ANGLES) 146 148 150 58: 270 type=129 (ANGLES) 146 148 154 58: 271 type=118 (ANGLES) 149 148 150 58: 272 type=116 (ANGLES) 149 148 154 58: 273 type=119 (ANGLES) 150 148 154 58: 274 type=118 (ANGLES) 148 150 151 58: 275 type=118 (ANGLES) 148 150 152 58: 276 type=118 (ANGLES) 148 150 153 58: 277 type=121 (ANGLES) 151 150 152 58: 278 type=121 (ANGLES) 151 150 153 58: 279 type=121 (ANGLES) 152 150 153 58: 280 type=122 (ANGLES) 148 154 155 58: G96Angle: 58: nr: 0 58: Restr. Angles: 58: nr: 0 58: Lin. Angle: 58: nr: 0 58: Bond-Cross: 58: nr: 0 58: BA-Cross: 58: nr: 0 58: U-B: 58: nr: 0 58: Quartic Angles: 58: nr: 0 58: Tab. Angles: 58: nr: 0 58: Proper Dih.: 58: nr: 145 58: iatoms: 58: 0 type=140 (PDIHS) 4 24 22 23 58: 1 type=141 (PDIHS) 22 26 24 25 58: 2 type=140 (PDIHS) 26 40 38 39 58: 3 type=141 (PDIHS) 38 42 40 41 58: 4 type=140 (PDIHS) 42 60 58 59 58: 5 type=142 (PDIHS) 44 47 50 48 58: 6 type=142 (PDIHS) 47 52 48 49 58: 7 type=142 (PDIHS) 47 54 50 51 58: 8 type=142 (PDIHS) 48 56 52 53 58: 9 type=142 (PDIHS) 50 56 54 55 58: 10 type=142 (PDIHS) 52 54 56 57 58: 11 type=141 (PDIHS) 58 62 60 61 58: 12 type=140 (PDIHS) 62 67 65 66 58: 13 type=141 (PDIHS) 65 69 67 68 58: 14 type=140 (PDIHS) 69 91 89 90 58: 15 type=141 (PDIHS) 77 82 80 81 58: 16 type=140 (PDIHS) 80 83 82 86 58: 17 type=141 (PDIHS) 82 84 83 85 58: 18 type=141 (PDIHS) 82 87 86 88 58: 19 type=141 (PDIHS) 89 93 91 92 58: 20 type=140 (PDIHS) 93 102 100 101 58: 21 type=141 (PDIHS) 100 104 102 103 58: 22 type=140 (PDIHS) 104 117 115 116 58: 23 type=140 (PDIHS) 109 113 112 114 58: 24 type=141 (PDIHS) 115 119 117 118 58: 25 type=140 (PDIHS) 119 136 134 135 58: 26 type=141 (PDIHS) 134 138 136 137 58: 27 type=140 (PDIHS) 138 146 144 145 58: 28 type=141 (PDIHS) 144 148 146 147 58: Ryckaert-Bell.: 58: nr: 1565 58: iatoms: 58: 0 type=143 (RBDIHS) 1 0 4 5 58: 1 type=144 (RBDIHS) 1 0 4 6 58: 2 type=144 (RBDIHS) 1 0 4 22 58: 3 type=143 (RBDIHS) 2 0 4 5 58: 4 type=144 (RBDIHS) 2 0 4 6 58: 5 type=144 (RBDIHS) 2 0 4 22 58: 6 type=143 (RBDIHS) 3 0 4 5 58: 7 type=144 (RBDIHS) 3 0 4 6 58: 8 type=144 (RBDIHS) 3 0 4 22 58: 9 type=145 (RBDIHS) 0 4 6 9 58: 10 type=146 (RBDIHS) 22 4 6 9 58: 11 type=147 (RBDIHS) 0 4 6 7 58: 12 type=147 (RBDIHS) 0 4 6 8 58: 13 type=148 (RBDIHS) 5 4 6 7 58: 14 type=148 (RBDIHS) 5 4 6 8 58: 15 type=148 (RBDIHS) 5 4 6 9 58: 16 type=149 (RBDIHS) 22 4 6 7 58: 17 type=149 (RBDIHS) 22 4 6 8 58: 18 type=150 (RBDIHS) 0 4 22 24 58: 19 type=151 (RBDIHS) 6 4 22 24 58: 20 type=148 (RBDIHS) 4 6 9 10 58: 21 type=148 (RBDIHS) 4 6 9 11 58: 22 type=152 (RBDIHS) 4 6 9 12 58: 23 type=148 (RBDIHS) 7 6 9 10 58: 24 type=148 (RBDIHS) 7 6 9 11 58: 25 type=148 (RBDIHS) 7 6 9 12 58: 26 type=148 (RBDIHS) 8 6 9 10 58: 27 type=148 (RBDIHS) 8 6 9 11 58: 28 type=148 (RBDIHS) 8 6 9 12 58: 29 type=148 (RBDIHS) 6 9 12 13 58: 30 type=148 (RBDIHS) 6 9 12 14 58: 31 type=152 (RBDIHS) 6 9 12 15 58: 32 type=148 (RBDIHS) 10 9 12 13 58: 33 type=148 (RBDIHS) 10 9 12 14 58: 34 type=148 (RBDIHS) 10 9 12 15 58: 35 type=148 (RBDIHS) 11 9 12 13 58: 36 type=148 (RBDIHS) 11 9 12 14 58: 37 type=148 (RBDIHS) 11 9 12 15 58: 38 type=148 (RBDIHS) 9 12 15 16 58: 39 type=148 (RBDIHS) 9 12 15 17 58: 40 type=153 (RBDIHS) 9 12 15 18 58: 41 type=148 (RBDIHS) 13 12 15 16 58: 42 type=148 (RBDIHS) 13 12 15 17 58: 43 type=154 (RBDIHS) 13 12 15 18 58: 44 type=148 (RBDIHS) 14 12 15 16 58: 45 type=148 (RBDIHS) 14 12 15 17 58: 46 type=154 (RBDIHS) 14 12 15 18 58: 47 type=144 (RBDIHS) 12 15 18 19 58: 48 type=144 (RBDIHS) 12 15 18 20 58: 49 type=144 (RBDIHS) 12 15 18 21 58: 50 type=143 (RBDIHS) 16 15 18 19 58: 51 type=143 (RBDIHS) 16 15 18 20 58: 52 type=143 (RBDIHS) 16 15 18 21 58: 53 type=143 (RBDIHS) 17 15 18 19 58: 54 type=143 (RBDIHS) 17 15 18 20 58: 55 type=143 (RBDIHS) 17 15 18 21 58: 56 type=155 (RBDIHS) 4 22 24 25 58: 57 type=156 (RBDIHS) 4 22 24 26 58: 58 type=155 (RBDIHS) 23 22 24 25 58: 59 type=157 (RBDIHS) 23 22 24 26 58: 60 type=158 (RBDIHS) 22 24 26 28 58: 61 type=159 (RBDIHS) 22 24 26 38 58: 62 type=160 (RBDIHS) 24 26 28 30 58: 63 type=160 (RBDIHS) 24 26 28 34 58: 64 type=161 (RBDIHS) 38 26 28 30 58: 65 type=161 (RBDIHS) 38 26 28 34 58: 66 type=147 (RBDIHS) 24 26 28 29 58: 67 type=148 (RBDIHS) 27 26 28 29 58: 68 type=148 (RBDIHS) 27 26 28 30 58: 69 type=148 (RBDIHS) 27 26 28 34 58: 70 type=149 (RBDIHS) 38 26 28 29 58: 71 type=150 (RBDIHS) 24 26 38 40 58: 72 type=151 (RBDIHS) 28 26 38 40 58: 73 type=148 (RBDIHS) 26 28 30 31 58: 74 type=148 (RBDIHS) 26 28 30 32 58: 75 type=148 (RBDIHS) 26 28 30 33 58: 76 type=148 (RBDIHS) 29 28 30 31 58: 77 type=148 (RBDIHS) 29 28 30 32 58: 78 type=148 (RBDIHS) 29 28 30 33 58: 79 type=148 (RBDIHS) 34 28 30 31 58: 80 type=148 (RBDIHS) 34 28 30 32 58: 81 type=148 (RBDIHS) 34 28 30 33 58: 82 type=148 (RBDIHS) 26 28 34 35 58: 83 type=148 (RBDIHS) 26 28 34 36 58: 84 type=148 (RBDIHS) 26 28 34 37 58: 85 type=148 (RBDIHS) 29 28 34 35 58: 86 type=148 (RBDIHS) 29 28 34 36 58: 87 type=148 (RBDIHS) 29 28 34 37 58: 88 type=148 (RBDIHS) 30 28 34 35 58: 89 type=148 (RBDIHS) 30 28 34 36 58: 90 type=148 (RBDIHS) 30 28 34 37 58: 91 type=155 (RBDIHS) 26 38 40 41 58: 92 type=156 (RBDIHS) 26 38 40 42 58: 93 type=155 (RBDIHS) 39 38 40 41 58: 94 type=157 (RBDIHS) 39 38 40 42 58: 95 type=158 (RBDIHS) 38 40 42 44 58: 96 type=159 (RBDIHS) 38 40 42 58 58: 97 type=147 (RBDIHS) 40 42 44 45 58: 98 type=147 (RBDIHS) 40 42 44 46 58: 99 type=162 (RBDIHS) 40 42 44 47 58: 100 type=148 (RBDIHS) 43 42 44 45 58: 101 type=148 (RBDIHS) 43 42 44 46 58: 102 type=163 (RBDIHS) 43 42 44 47 58: 103 type=149 (RBDIHS) 58 42 44 45 58: 104 type=149 (RBDIHS) 58 42 44 46 58: 105 type=164 (RBDIHS) 58 42 44 47 58: 106 type=150 (RBDIHS) 40 42 58 60 58: 107 type=151 (RBDIHS) 44 42 58 60 58: 108 type=165 (RBDIHS) 44 47 48 49 58: 109 type=165 (RBDIHS) 44 47 48 52 58: 110 type=165 (RBDIHS) 50 47 48 49 58: 111 type=165 (RBDIHS) 50 47 48 52 58: 112 type=165 (RBDIHS) 44 47 50 51 58: 113 type=165 (RBDIHS) 44 47 50 54 58: 114 type=165 (RBDIHS) 48 47 50 51 58: 115 type=165 (RBDIHS) 48 47 50 54 58: 116 type=165 (RBDIHS) 47 48 52 53 58: 117 type=165 (RBDIHS) 47 48 52 56 58: 118 type=165 (RBDIHS) 49 48 52 53 58: 119 type=165 (RBDIHS) 49 48 52 56 58: 120 type=165 (RBDIHS) 47 50 54 55 58: 121 type=165 (RBDIHS) 47 50 54 56 58: 122 type=165 (RBDIHS) 51 50 54 55 58: 123 type=165 (RBDIHS) 51 50 54 56 58: 124 type=165 (RBDIHS) 48 52 56 54 58: 125 type=165 (RBDIHS) 48 52 56 57 58: 126 type=165 (RBDIHS) 53 52 56 54 58: 127 type=165 (RBDIHS) 53 52 56 57 58: 128 type=165 (RBDIHS) 50 54 56 52 58: 129 type=165 (RBDIHS) 50 54 56 57 58: 130 type=165 (RBDIHS) 55 54 56 52 58: 131 type=165 (RBDIHS) 55 54 56 57 58: 132 type=155 (RBDIHS) 42 58 60 61 58: 133 type=156 (RBDIHS) 42 58 60 62 58: 134 type=155 (RBDIHS) 59 58 60 61 58: 135 type=157 (RBDIHS) 59 58 60 62 58: 136 type=159 (RBDIHS) 58 60 62 65 58: 137 type=150 (RBDIHS) 60 62 65 67 58: 138 type=155 (RBDIHS) 62 65 67 68 58: 139 type=156 (RBDIHS) 62 65 67 69 58: 140 type=155 (RBDIHS) 66 65 67 68 58: 141 type=157 (RBDIHS) 66 65 67 69 58: 142 type=158 (RBDIHS) 65 67 69 71 58: 143 type=159 (RBDIHS) 65 67 69 89 58: 144 type=166 (RBDIHS) 67 69 71 74 58: 145 type=167 (RBDIHS) 89 69 71 74 58: 146 type=147 (RBDIHS) 67 69 71 72 58: 147 type=147 (RBDIHS) 67 69 71 73 58: 148 type=148 (RBDIHS) 70 69 71 72 58: 149 type=148 (RBDIHS) 70 69 71 73 58: 150 type=148 (RBDIHS) 70 69 71 74 58: 151 type=149 (RBDIHS) 89 69 71 72 58: 152 type=149 (RBDIHS) 89 69 71 73 58: 153 type=150 (RBDIHS) 67 69 89 91 58: 154 type=151 (RBDIHS) 71 69 89 91 58: 155 type=148 (RBDIHS) 69 71 74 75 58: 156 type=148 (RBDIHS) 69 71 74 76 58: 157 type=152 (RBDIHS) 69 71 74 77 58: 158 type=148 (RBDIHS) 72 71 74 75 58: 159 type=148 (RBDIHS) 72 71 74 76 58: 160 type=148 (RBDIHS) 72 71 74 77 58: 161 type=148 (RBDIHS) 73 71 74 75 58: 162 type=148 (RBDIHS) 73 71 74 76 58: 163 type=148 (RBDIHS) 73 71 74 77 58: 164 type=148 (RBDIHS) 71 74 77 78 58: 165 type=148 (RBDIHS) 71 74 77 79 58: 166 type=153 (RBDIHS) 71 74 77 80 58: 167 type=148 (RBDIHS) 75 74 77 78 58: 168 type=148 (RBDIHS) 75 74 77 79 58: 169 type=168 (RBDIHS) 75 74 77 80 58: 170 type=148 (RBDIHS) 76 74 77 78 58: 171 type=148 (RBDIHS) 76 74 77 79 58: 172 type=168 (RBDIHS) 76 74 77 80 58: 173 type=169 (RBDIHS) 74 77 80 81 58: 174 type=170 (RBDIHS) 74 77 80 82 58: 175 type=171 (RBDIHS) 78 77 80 82 58: 176 type=171 (RBDIHS) 79 77 80 82 58: 177 type=172 (RBDIHS) 77 80 82 83 58: 178 type=172 (RBDIHS) 77 80 82 86 58: 179 type=173 (RBDIHS) 81 80 82 83 58: 180 type=173 (RBDIHS) 81 80 82 86 58: 181 type=173 (RBDIHS) 80 82 83 84 58: 182 type=173 (RBDIHS) 80 82 83 85 58: 183 type=173 (RBDIHS) 86 82 83 84 58: 184 type=173 (RBDIHS) 86 82 83 85 58: 185 type=173 (RBDIHS) 80 82 86 87 58: 186 type=173 (RBDIHS) 80 82 86 88 58: 187 type=173 (RBDIHS) 83 82 86 87 58: 188 type=173 (RBDIHS) 83 82 86 88 58: 189 type=155 (RBDIHS) 69 89 91 92 58: 190 type=156 (RBDIHS) 69 89 91 93 58: 191 type=155 (RBDIHS) 90 89 91 92 58: 192 type=157 (RBDIHS) 90 89 91 93 58: 193 type=158 (RBDIHS) 89 91 93 95 58: 194 type=159 (RBDIHS) 89 91 93 100 58: 195 type=174 (RBDIHS) 91 93 95 98 58: 196 type=175 (RBDIHS) 100 93 95 98 58: 197 type=147 (RBDIHS) 91 93 95 96 58: 198 type=147 (RBDIHS) 91 93 95 97 58: 199 type=148 (RBDIHS) 94 93 95 96 58: 200 type=148 (RBDIHS) 94 93 95 97 58: 201 type=176 (RBDIHS) 94 93 95 98 58: 202 type=149 (RBDIHS) 100 93 95 96 58: 203 type=149 (RBDIHS) 100 93 95 97 58: 204 type=150 (RBDIHS) 91 93 100 102 58: 205 type=151 (RBDIHS) 95 93 100 102 58: 206 type=177 (RBDIHS) 93 95 98 99 58: 207 type=178 (RBDIHS) 96 95 98 99 58: 208 type=178 (RBDIHS) 97 95 98 99 58: 209 type=155 (RBDIHS) 93 100 102 103 58: 210 type=156 (RBDIHS) 93 100 102 104 58: 211 type=155 (RBDIHS) 101 100 102 103 58: 212 type=157 (RBDIHS) 101 100 102 104 58: 213 type=158 (RBDIHS) 100 102 104 106 58: 214 type=159 (RBDIHS) 100 102 104 115 58: 215 type=179 (RBDIHS) 102 104 106 109 58: 216 type=180 (RBDIHS) 115 104 106 109 58: 217 type=147 (RBDIHS) 102 104 106 107 58: 218 type=147 (RBDIHS) 102 104 106 108 58: 219 type=148 (RBDIHS) 105 104 106 107 58: 220 type=148 (RBDIHS) 105 104 106 108 58: 221 type=148 (RBDIHS) 105 104 106 109 58: 222 type=149 (RBDIHS) 115 104 106 107 58: 223 type=149 (RBDIHS) 115 104 106 108 58: 224 type=150 (RBDIHS) 102 104 115 117 58: 225 type=151 (RBDIHS) 106 104 115 117 58: 226 type=148 (RBDIHS) 104 106 109 110 58: 227 type=148 (RBDIHS) 104 106 109 111 58: 228 type=181 (RBDIHS) 104 106 109 112 58: 229 type=148 (RBDIHS) 107 106 109 110 58: 230 type=148 (RBDIHS) 107 106 109 111 58: 231 type=182 (RBDIHS) 107 106 109 112 58: 232 type=148 (RBDIHS) 108 106 109 110 58: 233 type=148 (RBDIHS) 108 106 109 111 58: 234 type=182 (RBDIHS) 108 106 109 112 58: 235 type=183 (RBDIHS) 106 109 112 113 58: 236 type=183 (RBDIHS) 106 109 112 114 58: 237 type=155 (RBDIHS) 104 115 117 118 58: 238 type=156 (RBDIHS) 104 115 117 119 58: 239 type=155 (RBDIHS) 116 115 117 118 58: 240 type=157 (RBDIHS) 116 115 117 119 58: 241 type=158 (RBDIHS) 115 117 119 121 58: 242 type=159 (RBDIHS) 115 117 119 134 58: 243 type=184 (RBDIHS) 117 119 121 124 58: 244 type=185 (RBDIHS) 134 119 121 124 58: 245 type=147 (RBDIHS) 117 119 121 122 58: 246 type=147 (RBDIHS) 117 119 121 123 58: 247 type=148 (RBDIHS) 120 119 121 122 58: 248 type=148 (RBDIHS) 120 119 121 123 58: 249 type=148 (RBDIHS) 120 119 121 124 58: 250 type=149 (RBDIHS) 134 119 121 122 58: 251 type=149 (RBDIHS) 134 119 121 123 58: 252 type=150 (RBDIHS) 117 119 134 136 58: 253 type=151 (RBDIHS) 121 119 134 136 58: 254 type=148 (RBDIHS) 119 121 124 125 58: 255 type=152 (RBDIHS) 119 121 124 126 58: 256 type=152 (RBDIHS) 119 121 124 130 58: 257 type=148 (RBDIHS) 122 121 124 125 58: 258 type=148 (RBDIHS) 122 121 124 126 58: 259 type=148 (RBDIHS) 122 121 124 130 58: 260 type=148 (RBDIHS) 123 121 124 125 58: 261 type=148 (RBDIHS) 123 121 124 126 58: 262 type=148 (RBDIHS) 123 121 124 130 58: 263 type=148 (RBDIHS) 121 124 126 127 58: 264 type=148 (RBDIHS) 121 124 126 128 58: 265 type=148 (RBDIHS) 121 124 126 129 58: 266 type=148 (RBDIHS) 125 124 126 127 58: 267 type=148 (RBDIHS) 125 124 126 128 58: 268 type=148 (RBDIHS) 125 124 126 129 58: 269 type=148 (RBDIHS) 130 124 126 127 58: 270 type=148 (RBDIHS) 130 124 126 128 58: 271 type=148 (RBDIHS) 130 124 126 129 58: 272 type=148 (RBDIHS) 121 124 130 131 58: 273 type=148 (RBDIHS) 121 124 130 132 58: 274 type=148 (RBDIHS) 121 124 130 133 58: 275 type=148 (RBDIHS) 125 124 130 131 58: 276 type=148 (RBDIHS) 125 124 130 132 58: 277 type=148 (RBDIHS) 125 124 130 133 58: 278 type=148 (RBDIHS) 126 124 130 131 58: 279 type=148 (RBDIHS) 126 124 130 132 58: 280 type=148 (RBDIHS) 126 124 130 133 58: 281 type=155 (RBDIHS) 119 134 136 137 58: 282 type=156 (RBDIHS) 119 134 136 138 58: 283 type=155 (RBDIHS) 135 134 136 137 58: 284 type=157 (RBDIHS) 135 134 136 138 58: 285 type=158 (RBDIHS) 134 136 138 140 58: 286 type=159 (RBDIHS) 134 136 138 144 58: 287 type=147 (RBDIHS) 136 138 140 141 58: 288 type=147 (RBDIHS) 136 138 140 142 58: 289 type=147 (RBDIHS) 136 138 140 143 58: 290 type=148 (RBDIHS) 139 138 140 141 58: 291 type=148 (RBDIHS) 139 138 140 142 58: 292 type=148 (RBDIHS) 139 138 140 143 58: 293 type=149 (RBDIHS) 144 138 140 141 58: 294 type=149 (RBDIHS) 144 138 140 142 58: 295 type=149 (RBDIHS) 144 138 140 143 58: 296 type=150 (RBDIHS) 136 138 144 146 58: 297 type=151 (RBDIHS) 140 138 144 146 58: 298 type=155 (RBDIHS) 138 144 146 147 58: 299 type=156 (RBDIHS) 138 144 146 148 58: 300 type=155 (RBDIHS) 145 144 146 147 58: 301 type=157 (RBDIHS) 145 144 146 148 58: 302 type=158 (RBDIHS) 144 146 148 150 58: 303 type=159 (RBDIHS) 144 146 148 154 58: 304 type=147 (RBDIHS) 146 148 150 151 58: 305 type=147 (RBDIHS) 146 148 150 152 58: 306 type=147 (RBDIHS) 146 148 150 153 58: 307 type=148 (RBDIHS) 149 148 150 151 58: 308 type=148 (RBDIHS) 149 148 150 152 58: 309 type=148 (RBDIHS) 149 148 150 153 58: 310 type=149 (RBDIHS) 154 148 150 151 58: 311 type=149 (RBDIHS) 154 148 150 152 58: 312 type=149 (RBDIHS) 154 148 150 153 58: Restr. Dih.: 58: nr: 0 58: CBT Dih.: 58: nr: 0 58: Fourier Dih.: 58: nr: 0 58: Improper Dih.: 58: nr: 0 58: Per. Imp. Dih.: 58: nr: 0 58: Tab. Dih.: 58: nr: 0 58: CMAP Dih.: 58: nr: 0 58: GB 1-2 Pol.: 58: nr: 0 58: GB 1-3 Pol.: 58: nr: 0 58: GB 1-4 Pol.: 58: nr: 0 58: GB Polariz.: 58: nr: 0 58: Nonpolar Sol.: 58: nr: 0 58: LJ-14: 58: nr: 1197 58: iatoms: 58: 0 type=186 (LJ14) 0 7 58: 1 type=186 (LJ14) 0 8 58: 2 type=187 (LJ14) 0 9 58: 3 type=188 (LJ14) 0 23 58: 4 type=189 (LJ14) 0 24 58: 5 type=190 (LJ14) 1 5 58: 6 type=190 (LJ14) 1 6 58: 7 type=190 (LJ14) 1 22 58: 8 type=190 (LJ14) 2 5 58: 9 type=190 (LJ14) 2 6 58: 10 type=190 (LJ14) 2 22 58: 11 type=190 (LJ14) 3 5 58: 12 type=190 (LJ14) 3 6 58: 13 type=190 (LJ14) 3 22 58: 14 type=191 (LJ14) 4 10 58: 15 type=191 (LJ14) 4 11 58: 16 type=192 (LJ14) 4 12 58: 17 type=190 (LJ14) 4 25 58: 18 type=192 (LJ14) 4 26 58: 19 type=193 (LJ14) 5 7 58: 20 type=193 (LJ14) 5 8 58: 21 type=191 (LJ14) 5 9 58: 22 type=194 (LJ14) 5 23 58: 23 type=186 (LJ14) 5 24 58: 24 type=191 (LJ14) 6 13 58: 25 type=191 (LJ14) 6 14 58: 26 type=192 (LJ14) 6 15 58: 27 type=195 (LJ14) 6 23 58: 28 type=187 (LJ14) 6 24 58: 29 type=193 (LJ14) 7 10 58: 30 type=193 (LJ14) 7 11 58: 31 type=191 (LJ14) 7 12 58: 32 type=196 (LJ14) 7 22 58: 33 type=193 (LJ14) 8 10 58: 34 type=193 (LJ14) 8 11 58: 35 type=191 (LJ14) 8 12 58: 36 type=196 (LJ14) 8 22 58: 37 type=191 (LJ14) 9 16 58: 38 type=191 (LJ14) 9 17 58: 39 type=187 (LJ14) 9 18 58: 40 type=197 (LJ14) 9 22 58: 41 type=193 (LJ14) 10 13 58: 42 type=193 (LJ14) 10 14 58: 43 type=191 (LJ14) 10 15 58: 44 type=193 (LJ14) 11 13 58: 45 type=193 (LJ14) 11 14 58: 46 type=191 (LJ14) 11 15 58: 47 type=190 (LJ14) 12 19 58: 48 type=190 (LJ14) 12 20 58: 49 type=190 (LJ14) 12 21 58: 50 type=193 (LJ14) 13 16 58: 51 type=193 (LJ14) 13 17 58: 52 type=186 (LJ14) 13 18 58: 53 type=193 (LJ14) 14 16 58: 54 type=193 (LJ14) 14 17 58: 55 type=186 (LJ14) 14 18 58: 56 type=190 (LJ14) 16 19 58: 57 type=190 (LJ14) 16 20 58: 58 type=190 (LJ14) 16 21 58: 59 type=190 (LJ14) 17 19 58: 60 type=190 (LJ14) 17 20 58: 61 type=190 (LJ14) 17 21 58: 62 type=196 (LJ14) 22 27 58: 63 type=197 (LJ14) 22 28 58: 64 type=198 (LJ14) 22 38 58: 65 type=190 (LJ14) 23 25 58: 66 type=195 (LJ14) 23 26 58: 67 type=186 (LJ14) 24 29 58: 68 type=187 (LJ14) 24 30 58: 69 type=187 (LJ14) 24 34 58: 70 type=188 (LJ14) 24 39 58: 71 type=189 (LJ14) 24 40 58: 72 type=190 (LJ14) 25 27 58: 73 type=190 (LJ14) 25 28 58: 74 type=190 (LJ14) 25 38 58: 75 type=191 (LJ14) 26 31 58: 76 type=191 (LJ14) 26 32 58: 77 type=191 (LJ14) 26 33 58: 78 type=191 (LJ14) 26 35 58: 79 type=191 (LJ14) 26 36 58: 80 type=191 (LJ14) 26 37 58: 81 type=190 (LJ14) 26 41 58: 82 type=192 (LJ14) 26 42 58: 83 type=193 (LJ14) 27 29 58: 84 type=191 (LJ14) 27 30 58: 85 type=191 (LJ14) 27 34 58: 86 type=194 (LJ14) 27 39 58: 87 type=186 (LJ14) 27 40 58: 88 type=195 (LJ14) 28 39 58: 89 type=187 (LJ14) 28 40 58: 90 type=193 (LJ14) 29 31 58: 91 type=193 (LJ14) 29 32 58: 92 type=193 (LJ14) 29 33 58: 93 type=193 (LJ14) 29 35 58: 94 type=193 (LJ14) 29 36 58: 95 type=193 (LJ14) 29 37 58: 96 type=196 (LJ14) 29 38 58: 97 type=191 (LJ14) 30 35 58: 98 type=191 (LJ14) 30 36 58: 99 type=191 (LJ14) 30 37 58: 100 type=197 (LJ14) 30 38 58: 101 type=191 (LJ14) 31 34 58: 102 type=191 (LJ14) 32 34 58: 103 type=191 (LJ14) 33 34 58: 104 type=197 (LJ14) 34 38 58: 105 type=196 (LJ14) 38 43 58: 106 type=197 (LJ14) 38 44 58: 107 type=198 (LJ14) 38 58 58: 108 type=190 (LJ14) 39 41 58: 109 type=195 (LJ14) 39 42 58: 110 type=186 (LJ14) 40 45 58: 111 type=186 (LJ14) 40 46 58: 112 type=199 (LJ14) 40 47 58: 113 type=188 (LJ14) 40 59 58: 114 type=189 (LJ14) 40 60 58: 115 type=190 (LJ14) 41 43 58: 116 type=190 (LJ14) 41 44 58: 117 type=190 (LJ14) 41 58 58: 118 type=200 (LJ14) 42 48 58: 119 type=200 (LJ14) 42 50 58: 120 type=190 (LJ14) 42 61 58: 121 type=192 (LJ14) 42 62 58: 122 type=193 (LJ14) 43 45 58: 123 type=193 (LJ14) 43 46 58: 124 type=201 (LJ14) 43 47 58: 125 type=194 (LJ14) 43 59 58: 126 type=186 (LJ14) 43 60 58: 127 type=202 (LJ14) 44 49 58: 128 type=202 (LJ14) 44 51 58: 129 type=200 (LJ14) 44 52 58: 130 type=200 (LJ14) 44 54 58: 131 type=195 (LJ14) 44 59 58: 132 type=187 (LJ14) 44 60 58: 133 type=201 (LJ14) 45 48 58: 134 type=201 (LJ14) 45 50 58: 135 type=196 (LJ14) 45 58 58: 136 type=201 (LJ14) 46 48 58: 137 type=201 (LJ14) 46 50 58: 138 type=196 (LJ14) 46 58 58: 139 type=203 (LJ14) 47 53 58: 140 type=203 (LJ14) 47 55 58: 141 type=204 (LJ14) 47 56 58: 142 type=205 (LJ14) 47 58 58: 143 type=203 (LJ14) 48 51 58: 144 type=204 (LJ14) 48 54 58: 145 type=203 (LJ14) 48 57 58: 146 type=203 (LJ14) 49 50 58: 147 type=206 (LJ14) 49 53 58: 148 type=203 (LJ14) 49 56 58: 149 type=204 (LJ14) 50 52 58: 150 type=203 (LJ14) 50 57 58: 151 type=206 (LJ14) 51 55 58: 152 type=203 (LJ14) 51 56 58: 153 type=203 (LJ14) 52 55 58: 154 type=203 (LJ14) 53 54 58: 155 type=206 (LJ14) 53 57 58: 156 type=206 (LJ14) 55 57 58: 157 type=196 (LJ14) 58 63 58: 158 type=196 (LJ14) 58 64 58: 159 type=198 (LJ14) 58 65 58: 160 type=190 (LJ14) 59 61 58: 161 type=195 (LJ14) 59 62 58: 162 type=188 (LJ14) 60 66 58: 163 type=189 (LJ14) 60 67 58: 164 type=190 (LJ14) 61 63 58: 165 type=190 (LJ14) 61 64 58: 166 type=190 (LJ14) 61 65 58: 167 type=190 (LJ14) 62 68 58: 168 type=192 (LJ14) 62 69 58: 169 type=194 (LJ14) 63 66 58: 170 type=186 (LJ14) 63 67 58: 171 type=194 (LJ14) 64 66 58: 172 type=186 (LJ14) 64 67 58: 173 type=196 (LJ14) 65 70 58: 174 type=197 (LJ14) 65 71 58: 175 type=198 (LJ14) 65 89 58: 176 type=190 (LJ14) 66 68 58: 177 type=195 (LJ14) 66 69 58: 178 type=186 (LJ14) 67 72 58: 179 type=186 (LJ14) 67 73 58: 180 type=187 (LJ14) 67 74 58: 181 type=188 (LJ14) 67 90 58: 182 type=189 (LJ14) 67 91 58: 183 type=190 (LJ14) 68 70 58: 184 type=190 (LJ14) 68 71 58: 185 type=190 (LJ14) 68 89 58: 186 type=191 (LJ14) 69 75 58: 187 type=191 (LJ14) 69 76 58: 188 type=192 (LJ14) 69 77 58: 189 type=190 (LJ14) 69 92 58: 190 type=192 (LJ14) 69 93 58: 191 type=193 (LJ14) 70 72 58: 192 type=193 (LJ14) 70 73 58: 193 type=191 (LJ14) 70 74 58: 194 type=194 (LJ14) 70 90 58: 195 type=186 (LJ14) 70 91 58: 196 type=191 (LJ14) 71 78 58: 197 type=191 (LJ14) 71 79 58: 198 type=187 (LJ14) 71 80 58: 199 type=195 (LJ14) 71 90 58: 200 type=187 (LJ14) 71 91 58: 201 type=193 (LJ14) 72 75 58: 202 type=193 (LJ14) 72 76 58: 203 type=191 (LJ14) 72 77 58: 204 type=196 (LJ14) 72 89 58: 205 type=193 (LJ14) 73 75 58: 206 type=193 (LJ14) 73 76 58: 207 type=191 (LJ14) 73 77 58: 208 type=196 (LJ14) 73 89 58: 209 type=190 (LJ14) 74 81 58: 210 type=207 (LJ14) 74 82 58: 211 type=197 (LJ14) 74 89 58: 212 type=193 (LJ14) 75 78 58: 213 type=193 (LJ14) 75 79 58: 214 type=186 (LJ14) 75 80 58: 215 type=193 (LJ14) 76 78 58: 216 type=193 (LJ14) 76 79 58: 217 type=186 (LJ14) 76 80 58: 218 type=187 (LJ14) 77 83 58: 219 type=187 (LJ14) 77 86 58: 220 type=190 (LJ14) 78 81 58: 221 type=208 (LJ14) 78 82 58: 222 type=190 (LJ14) 79 81 58: 223 type=208 (LJ14) 79 82 58: 224 type=190 (LJ14) 80 84 58: 225 type=190 (LJ14) 80 85 58: 226 type=190 (LJ14) 80 87 58: 227 type=190 (LJ14) 80 88 58: 228 type=190 (LJ14) 81 83 58: 229 type=190 (LJ14) 81 86 58: 230 type=190 (LJ14) 83 87 58: 231 type=190 (LJ14) 83 88 58: 232 type=190 (LJ14) 84 86 58: 233 type=190 (LJ14) 85 86 58: 234 type=196 (LJ14) 89 94 58: 235 type=197 (LJ14) 89 95 58: 236 type=198 (LJ14) 89 100 58: 237 type=190 (LJ14) 90 92 58: 238 type=195 (LJ14) 90 93 58: 239 type=186 (LJ14) 91 96 58: 240 type=186 (LJ14) 91 97 58: 241 type=209 (LJ14) 91 98 58: 242 type=188 (LJ14) 91 101 58: 243 type=189 (LJ14) 91 102 58: 244 type=190 (LJ14) 92 94 58: 245 type=190 (LJ14) 92 95 58: 246 type=190 (LJ14) 92 100 58: 247 type=190 (LJ14) 93 99 58: 248 type=190 (LJ14) 93 103 58: 249 type=192 (LJ14) 93 104 58: 250 type=193 (LJ14) 94 96 58: 251 type=193 (LJ14) 94 97 58: 252 type=210 (LJ14) 94 98 58: 253 type=194 (LJ14) 94 101 58: 254 type=186 (LJ14) 94 102 58: 255 type=195 (LJ14) 95 101 58: 256 type=187 (LJ14) 95 102 58: 257 type=190 (LJ14) 96 99 58: 258 type=196 (LJ14) 96 100 58: 259 type=190 (LJ14) 97 99 58: 260 type=196 (LJ14) 97 100 58: 261 type=211 (LJ14) 98 100 58: 262 type=196 (LJ14) 100 105 58: 263 type=197 (LJ14) 100 106 58: 264 type=198 (LJ14) 100 115 58: 265 type=190 (LJ14) 101 103 58: 266 type=195 (LJ14) 101 104 58: 267 type=186 (LJ14) 102 107 58: 268 type=186 (LJ14) 102 108 58: 269 type=187 (LJ14) 102 109 58: 270 type=188 (LJ14) 102 116 58: 271 type=189 (LJ14) 102 117 58: 272 type=190 (LJ14) 103 105 58: 273 type=190 (LJ14) 103 106 58: 274 type=190 (LJ14) 103 115 58: 275 type=191 (LJ14) 104 110 58: 276 type=191 (LJ14) 104 111 58: 277 type=197 (LJ14) 104 112 58: 278 type=190 (LJ14) 104 118 58: 279 type=192 (LJ14) 104 119 58: 280 type=193 (LJ14) 105 107 58: 281 type=193 (LJ14) 105 108 58: 282 type=191 (LJ14) 105 109 58: 283 type=194 (LJ14) 105 116 58: 284 type=186 (LJ14) 105 117 58: 285 type=195 (LJ14) 106 113 58: 286 type=195 (LJ14) 106 114 58: 287 type=195 (LJ14) 106 116 58: 288 type=187 (LJ14) 106 117 58: 289 type=193 (LJ14) 107 110 58: 290 type=193 (LJ14) 107 111 58: 291 type=196 (LJ14) 107 112 58: 292 type=196 (LJ14) 107 115 58: 293 type=193 (LJ14) 108 110 58: 294 type=193 (LJ14) 108 111 58: 295 type=196 (LJ14) 108 112 58: 296 type=196 (LJ14) 108 115 58: 297 type=197 (LJ14) 109 115 58: 298 type=194 (LJ14) 110 113 58: 299 type=194 (LJ14) 110 114 58: 300 type=194 (LJ14) 111 113 58: 301 type=194 (LJ14) 111 114 58: 302 type=196 (LJ14) 115 120 58: 303 type=197 (LJ14) 115 121 58: 304 type=198 (LJ14) 115 134 58: 305 type=190 (LJ14) 116 118 58: 306 type=195 (LJ14) 116 119 58: 307 type=186 (LJ14) 117 122 58: 308 type=186 (LJ14) 117 123 58: 309 type=187 (LJ14) 117 124 58: 310 type=188 (LJ14) 117 135 58: 311 type=189 (LJ14) 117 136 58: 312 type=190 (LJ14) 118 120 58: 313 type=190 (LJ14) 118 121 58: 314 type=190 (LJ14) 118 134 58: 315 type=191 (LJ14) 119 125 58: 316 type=192 (LJ14) 119 126 58: 317 type=192 (LJ14) 119 130 58: 318 type=190 (LJ14) 119 137 58: 319 type=192 (LJ14) 119 138 58: 320 type=193 (LJ14) 120 122 58: 321 type=193 (LJ14) 120 123 58: 322 type=191 (LJ14) 120 124 58: 323 type=194 (LJ14) 120 135 58: 324 type=186 (LJ14) 120 136 58: 325 type=191 (LJ14) 121 127 58: 326 type=191 (LJ14) 121 128 58: 327 type=191 (LJ14) 121 129 58: 328 type=191 (LJ14) 121 131 58: 329 type=191 (LJ14) 121 132 58: 330 type=191 (LJ14) 121 133 58: 331 type=195 (LJ14) 121 135 58: 332 type=187 (LJ14) 121 136 58: 333 type=193 (LJ14) 122 125 58: 334 type=191 (LJ14) 122 126 58: 335 type=191 (LJ14) 122 130 58: 336 type=196 (LJ14) 122 134 58: 337 type=193 (LJ14) 123 125 58: 338 type=191 (LJ14) 123 126 58: 339 type=191 (LJ14) 123 130 58: 340 type=196 (LJ14) 123 134 58: 341 type=197 (LJ14) 124 134 58: 342 type=193 (LJ14) 125 127 58: 343 type=193 (LJ14) 125 128 58: 344 type=193 (LJ14) 125 129 58: 345 type=193 (LJ14) 125 131 58: 346 type=193 (LJ14) 125 132 58: 347 type=193 (LJ14) 125 133 58: 348 type=191 (LJ14) 126 131 58: 349 type=191 (LJ14) 126 132 58: 350 type=191 (LJ14) 126 133 58: 351 type=191 (LJ14) 127 130 58: 352 type=191 (LJ14) 128 130 58: 353 type=191 (LJ14) 129 130 58: 354 type=196 (LJ14) 134 139 58: 355 type=197 (LJ14) 134 140 58: 356 type=198 (LJ14) 134 144 58: 357 type=190 (LJ14) 135 137 58: 358 type=195 (LJ14) 135 138 58: 359 type=186 (LJ14) 136 141 58: 360 type=186 (LJ14) 136 142 58: 361 type=186 (LJ14) 136 143 58: 362 type=188 (LJ14) 136 145 58: 363 type=189 (LJ14) 136 146 58: 364 type=190 (LJ14) 137 139 58: 365 type=190 (LJ14) 137 140 58: 366 type=190 (LJ14) 137 144 58: 367 type=190 (LJ14) 138 147 58: 368 type=192 (LJ14) 138 148 58: 369 type=193 (LJ14) 139 141 58: 370 type=193 (LJ14) 139 142 58: 371 type=193 (LJ14) 139 143 58: 372 type=194 (LJ14) 139 145 58: 373 type=186 (LJ14) 139 146 58: 374 type=195 (LJ14) 140 145 58: 375 type=187 (LJ14) 140 146 58: 376 type=196 (LJ14) 141 144 58: 377 type=196 (LJ14) 142 144 58: 378 type=196 (LJ14) 143 144 58: 379 type=196 (LJ14) 144 149 58: 380 type=197 (LJ14) 144 150 58: 381 type=198 (LJ14) 144 154 58: 382 type=190 (LJ14) 145 147 58: 383 type=195 (LJ14) 145 148 58: 384 type=186 (LJ14) 146 151 58: 385 type=186 (LJ14) 146 152 58: 386 type=186 (LJ14) 146 153 58: 387 type=188 (LJ14) 146 155 58: 388 type=190 (LJ14) 147 149 58: 389 type=190 (LJ14) 147 150 58: 390 type=190 (LJ14) 147 154 58: 391 type=193 (LJ14) 149 151 58: 392 type=193 (LJ14) 149 152 58: 393 type=193 (LJ14) 149 153 58: 394 type=194 (LJ14) 149 155 58: 395 type=195 (LJ14) 150 155 58: 396 type=196 (LJ14) 151 154 58: 397 type=196 (LJ14) 152 154 58: 398 type=196 (LJ14) 153 154 58: Coulomb-14: 58: nr: 0 58: LJC-14 q: 58: nr: 0 58: LJC Pairs NB: 58: nr: 0 58: LJ (SR): 58: nr: 0 58: Buck.ham (SR): 58: nr: 0 58: LJ: 58: nr: 0 58: B.ham: 58: nr: 0 58: Disper. corr.: 58: nr: 0 58: Coulomb (SR): 58: nr: 0 58: Coul: 58: nr: 0 58: RF excl.: 58: nr: 0 58: Coul. recip.: 58: nr: 0 58: LJ recip.: 58: nr: 0 58: DPD: 58: nr: 0 58: Polarization: 58: nr: 0 58: Water Pol.: 58: nr: 0 58: Thole Pol.: 58: nr: 0 58: Anharm. Pol.: 58: nr: 0 58: Position Rest.: 58: nr: 0 58: Flat-b. P-R.: 58: nr: 0 58: Dis. Rest.: 58: nr: 0 58: D.R.Viol. (nm): 58: nr: 0 58: Orient. Rest.: 58: nr: 0 58: Ori. R. RMSD: 58: nr: 0 58: Angle Rest.: 58: nr: 0 58: Angle Rest. Z: 58: nr: 0 58: Dih. Rest.: 58: nr: 0 58: Dih. Rest. Vi.: 58: nr: 0 58: Constraint: 58: nr: 0 58: Constr. No Co.: 58: nr: 0 58: Settle: 58: nr: 0 58: Virtual site 1: 58: nr: 0 58: Virtual site 2: 58: nr: 0 58: Virt. site 2fd: 58: nr: 0 58: Virtual site 3: 58: nr: 0 58: Virt. site 3fd: 58: nr: 0 58: Vir. site 3fad: 58: nr: 0 58: Vir. site 3out: 58: nr: 0 58: Virt. site 4fd: 58: nr: 0 58: Vir. site 4fdn: 58: nr: 0 58: Virtual site N: 58: nr: 0 58: COM Pull En.: 58: nr: 0 58: Dens. fitting: 58: nr: 0 58: Quantum En.: 58: nr: 0 58: Potential: 58: nr: 0 58: Kinetic En.: 58: nr: 0 58: Total Energy: 58: nr: 0 58: Conserved En.: 58: nr: 0 58: Temperature: 58: nr: 0 58: Vir. Temp.: 58: nr: 0 58: Pres. DC: 58: nr: 0 58: Pressure: 58: nr: 0 58: dH/dl constr.: 58: nr: 0 58: dVremain/dl: 58: nr: 0 58: dEkin/dl: 58: nr: 0 58: dVcoul/dl: 58: nr: 0 58: dVvdw/dl: 58: nr: 0 58: dVbonded/dl: 58: nr: 0 58: dVrestraint/dl: 58: nr: 0 58: dVtemp/dl: 58: nr: 0 58: grp[T-Coupling ] nr=1, name=[ rest] 58: grp[Energy Mon. ] nr=1, name=[ rest] 58: grp[Acc. not used] nr=1, name=[ rest] 58: grp[Freeze ] nr=1, name=[ rest] 58: grp[User1 ] nr=1, name=[ rest] 58: grp[User2 ] nr=1, name=[ rest] 58: grp[VCM ] nr=1, name=[ rest] 58: grp[Compressed X] nr=1, name=[ rest] 58: grp[Or. Res. Fit] nr=1, name=[ rest] 58: grp[QMMM ] nr=1, name=[ rest] 58: grpname (11): 58: grpname[0]={name="System"} 58: grpname[1]={name="Protein"} 58: grpname[2]={name="Protein-H"} 58: grpname[3]={name="C-alpha"} 58: grpname[4]={name="Backbone"} 58: grpname[5]={name="MainChain"} 58: grpname[6]={name="MainChain+Cb"} 58: grpname[7]={name="MainChain+H"} 58: grpname[8]={name="SideChain"} 58: grpname[9]={name="SideChain-H"} 58: grpname[10]={name="rest"} 58: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 58: allocated 0 0 0 0 0 0 0 0 0 0 58: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 58: box (3x3): 58: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 58: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 58: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 58: box_rel (3x3): 58: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv (3x3): 58: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev (3x3): 58: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev (3x3): 58: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev (3x3): 58: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: nosehoover_xi: not available 58: x (156x3): 58: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 58: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 58: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 58: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 58: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 58: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 58: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 58: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 58: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 58: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 58: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 58: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 58: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 58: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 58: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 58: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 58: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 58: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 58: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 58: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 58: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 58: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 58: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 58: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 58: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 58: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 58: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 58: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 58: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 58: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 58: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 58: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 58: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 58: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 58: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 58: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 58: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 58: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 58: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 58: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 58: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 58: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 58: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 58: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 58: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 58: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 58: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 58: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 58: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 58: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 58: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 58: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 58: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 58: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 58: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 58: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 58: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 58: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 58: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 58: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 58: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 58: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 58: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 58: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 58: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 58: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 58: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 58: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 58: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 58: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 58: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 58: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 58: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 58: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 58: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 58: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 58: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 58: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 58: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 58: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 58: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 58: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 58: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 58: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 58: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 58: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 58: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 58: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 58: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 58: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 58: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 58: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 58: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 58: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 58: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 58: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 58: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 58: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 58: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 58: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 58: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 58: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 58: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 58: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 58: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 58: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 58: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 58: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 58: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 58: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 58: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 58: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 58: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 58: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 58: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 58: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 58: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 58: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 58: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 58: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 58: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 58: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 58: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 58: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 58: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 58: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 58: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 58: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 58: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 58: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 58: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 58: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 58: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 58: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 58: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 58: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 58: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 58: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 58: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 58: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 58: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 58: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 58: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 58: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 58: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 58: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 58: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 58: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 58: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 58: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 58: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 58: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 58: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 58: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 58: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 58: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 58: v (156x3): 58: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: Group statistics 58: T-Coupling : 156 (total 156 atoms) 58: Energy Mon. : 156 (total 156 atoms) 58: Acc. not used: 156 (total 156 atoms) 58: Freeze : 156 (total 156 atoms) 58: User1 : 156 (total 156 atoms) 58: User2 : 156 (total 156 atoms) 58: VCM : 156 (total 156 atoms) 58: Compressed X: 156 (total 156 atoms) 58: Or. Res. Fit: 156 (total 156 atoms) 58: QMMM : 156 (total 156 atoms) 58: [ OK ] DumpTest.WorksWithTpr (65 ms) 58: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 58: [----------] 2 tests from DumpTest (66 ms total) 58: 58: [----------] 3 tests from HelpwritingTest 58: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 58: [ OK ] HelpwritingTest.ConvertTprWritesHelp (7 ms) 58: [ RUN ] HelpwritingTest.DumpWritesHelp 58: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 58: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 58: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (3 ms) 58: [----------] 3 tests from HelpwritingTest (11 ms total) 58: 58: [----------] 7 tests from GmxMakeNdx 58: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 16 Protein residues 58: Analysing Protein... 58: 58: 0 System : 256 atoms 58: 1 Protein : 256 atoms 58: 2 Protein-H : 139 atoms 58: 3 C-alpha : 16 atoms 58: 4 Backbone : 48 atoms 58: 5 MainChain : 63 atoms 58: 6 MainChain+Cb : 78 atoms 58: 7 MainChain+H : 81 atoms 58: 8 SideChain : 175 atoms 58: 9 SideChain-H : 76 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (13 ms) 58: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 58: Going to read 1 old index file(s) 58: Deducing 22 atoms in the system from indices in the index file 58: 58: 0 System : 22 atoms 58: 1 Protein : 22 atoms 58: 2 Protein-H : 10 atoms 58: 3 C-alpha : 1 atoms 58: 4 Backbone : 5 atoms 58: 5 MainChain : 7 atoms 58: 6 MainChain+Cb : 8 atoms 58: 7 MainChain+H : 9 atoms 58: 8 SideChain : 13 atoms 58: 9 SideChain-H : 3 atoms 58: 10 CA : 1 atoms 58: 11 C_&_r_1 : 1 atoms 58: 12 C_&_r_2 : 1 atoms 58: 13 N_&_r_2 : 1 atoms 58: 14 N_&_r_3 : 1 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Copied index group 1 'Protein' 58: Copied index group 2 'Protein-H' 58: Merged two groups with OR: 22 10 -> 22 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesNoStructureInput (6 ms) 58: [ RUN ] GmxMakeNdx.HandlesNotProtein 58: Going to read 1 old index file(s) 58: Deducing 6 atoms in the system from indices in the index file 58: 58: 0 System : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 58: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 58: Going to read 1 old index file(s) 58: Deducing 22 atoms in the system from indices in the index file 58: 58: 0 System : 22 atoms 58: 1 Protein : 22 atoms 58: 2 Protein-H : 10 atoms 58: 3 C-alpha : 1 atoms 58: 4 Backbone : 5 atoms 58: 5 MainChain : 7 atoms 58: 6 MainChain+Cb : 8 atoms 58: 7 MainChain+H : 9 atoms 58: 8 SideChain : 13 atoms 58: 9 SideChain-H : 3 atoms 58: 10 CA : 1 atoms 58: 11 C_&_r_1 : 1 atoms 58: 12 C_&_r_2 : 1 atoms 58: 13 N_&_r_2 : 1 atoms 58: 14 N_&_r_3 : 1 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Copied index group 4 'Backbone' 58: Copied index group 8 'SideChain' 58: Merged two groups with AND: 5 13 -> 0 58: Group is empty 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (5 ms) 58: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 58: Going to read 1 old index file(s) 58: Deducing 6 atoms in the system from indices in the index file 58: 58: 0 System : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Removed group 0 'System' 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 58: [ RUN ] GmxMakeNdx.Splitres 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 2 Water residues 58: 58: 0 System : 6 atoms 58: 1 Water : 6 atoms 58: 2 SOL : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Splitting group 1 'Water' into residues 58: 58: > 58: [ OK ] GmxMakeNdx.Splitres (0 ms) 58: [ RUN ] GmxMakeNdx.Splitat 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 2 Water residues 58: 58: 0 System : 6 atoms 58: 1 Water : 6 atoms 58: 2 SOL : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Splitting group 1 'Water' into atoms 58: 58: > 58: [ OK ] GmxMakeNdx.Splitat (12 ms) 58: [----------] 7 tests from GmxMakeNdx (40 ms total) 58: 58: [----------] 4 tests from ReportMethodsTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Setting the LD random seed to -564658305 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 58: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 58: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 58: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 58: [ RUN ] ReportMethodsTest.WritesCorrectInformation 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 58: [ RUN ] ReportMethodsTest.ToolEndToEndTest 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: section: Methods 58: subsection: Simulation system 58: A system of 1 molecules (156 atoms) was simulated. 58: 58: subsection: Simulation settings 58: A total of 0 ns were simulated with a time step of 1 fs. 58: Neighbor searching was performed every 10 steps. 58: The Cut-off algorithm was used for electrostatic interactions. 58: with a cut-off of 1 nm. 58: A single cut-off of 1.1 nm was used for Van der Waals interactions. 58: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 58: [----------] 4 tests from ReportMethodsTest (0 ms total) 58: 58: [----------] 4 tests from ConvertTprTest 58: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to 2147483647 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: Extending remaining runtime by 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: Extending remaining runtime by 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 200000 58: Runtime for the run 200 ps 58: Run end step 200000 58: Run end time 200 ps 58: 58: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (711 ms) 58: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -71303233 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: Extending remaining runtime to 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (750 ms) 58: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting nsteps to 102 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -555877001 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 102 58: Runtime for the run 0.102 ps 58: Run end step 102 58: Run end time 0.102 ps 58: 58: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (925 ms) 58: [ RUN ] ConvertTprTest.generateVelocitiesTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -35138340 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] ConvertTprTest.generateVelocitiesTest (787 ms) 58: [----------] 4 tests from ConvertTprTest (3174 ms total) 58: 58: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (32 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 58: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (36 ms total) 58: 58: [----------] 30 tests from Works/TrjconvDumpTest 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (20 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (22 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 58: [----------] 30 tests from Works/TrjconvDumpTest (50 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 62 tests from 7 test suites ran. (5078 ms total) 58: [ PASSED ] 62 tests. 58/87 Test #58: ToolUnitTests ............................. Passed 5.14 sec test 59 Start 59: FileIOTests 59: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/FileIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/fileio/tests 59: Test timeout computed to be: 30 59: [==========] Running 413 tests from 15 test suites. 59: [----------] Global test environment set-up. 59: [----------] 4 tests from Checkpoint 59: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 59: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (8 ms) 59: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 59: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 59: [ RUN ] Checkpoint.KvtRoundTripInt64 59: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 59: [ RUN ] Checkpoint.KvtRoundTripReal 59: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 59: [----------] 4 tests from Checkpoint (8 ms total) 59: 59: [----------] 1 test from StructureIOTest 59: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 59: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 59: [----------] 1 test from StructureIOTest (0 ms total) 59: 59: [----------] 2 tests from FileMD5Test 59: [ RUN ] FileMD5Test.CanComputeMD5 59: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 59: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 59: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 59: [----------] 2 tests from FileMD5Test (0 ms total) 59: 59: [----------] 4 tests from FileTypeTest 59: [ RUN ] FileTypeTest.CorrectValueForEmptyString 59: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForNoExtension 59: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 59: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 59: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 59: [----------] 4 tests from FileTypeTest (0 ms total) 59: 59: [----------] 3 tests from MrcSerializer 59: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 59: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 59: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 59: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 59: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 59: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 59: [----------] 3 tests from MrcSerializer (0 ms total) 59: 59: [----------] 4 tests from MrcDensityMap 59: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 59: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 59: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 59: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 59: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 59: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 59: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 59: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 59: [----------] 4 tests from MrcDensityMap (1 ms total) 59: 59: [----------] 8 tests from MrcDensityMapHeaderTest 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 59: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 59: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 59: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.IsSane 59: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 59: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 59: 59: [----------] 10 tests from ReadTest 59: [ RUN ] ReadTest.get_eint_ReadsInteger 59: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 59: 59: ERROR 1 [file unknown]: 59: Right hand side '0.8' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 59: [ RUN ] ReadTest.get_eint_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.get_eint64_ReadsInteger 59: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 59: 59: ERROR 1 [file unknown]: 59: Right hand side '0.8' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 59: [ RUN ] ReadTest.get_eint64_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.get_ereal_ReadsInteger 59: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_ereal_ReadsFloat 59: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 59: [ RUN ] ReadTest.get_ereal_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not a 59: real value 59: 59: 59: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 59: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 59: [----------] 10 tests from ReadTest (0 ms total) 59: 59: [----------] 3 tests from TimeControlTest 59: [ RUN ] TimeControlTest.UnSetHasNoValue 59: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 59: [ RUN ] TimeControlTest.CanSetValue 59: [ OK ] TimeControlTest.CanSetValue (0 ms) 59: [ RUN ] TimeControlTest.CanUnsetValueAgain 59: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 59: [----------] 3 tests from TimeControlTest (0 ms total) 59: 59: [----------] 1 test from FileIOXdrSerializerTest 59: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 59: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 59: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 59: 59: [----------] 1 test from TngTest 59: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 59: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 59: [----------] 1 test from TngTest (0 ms total) 59: 59: [----------] 4 tests from XvgioTest 59: [ RUN ] XvgioTest.readXvgIntWorks 59: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgRealWorks 59: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 59: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgDeprecatedWorks 59: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 59: [----------] 4 tests from XvgioTest (0 ms total) 59: 59: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 59: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 59: 59: [----------] 360 tests from FileTypeMatch/FileTypeTest 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 59: [----------] 360 tests from FileTypeMatch/FileTypeTest (1 ms total) 59: 59: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 59: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 413 tests from 15 test suites ran. (13 ms total) 59: [ PASSED ] 413 tests. 59/87 Test #59: FileIOTests ............................... Passed 0.06 sec test 60 Start 60: SelectionUnitTests 60: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/SelectionUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/gromacs/selection/tests 60: Test timeout computed to be: 30 60: [==========] Running 201 tests from 11 test suites. 60: [----------] Global test environment set-up. 60: [----------] 1 test from IndexGroupTest 60: [ RUN ] IndexGroupTest.RemovesDuplicates 60: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 60: [----------] 1 test from IndexGroupTest (0 ms total) 60: 60: [----------] 15 tests from IndexBlockTest 60: [ RUN ] IndexBlockTest.CreatesUnknownBlock 60: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 60: [ RUN ] IndexBlockTest.CreatesAtomBlock 60: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 60: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 60: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 60: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 60: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 60: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesSingleBlock 60: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 60: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 60: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 60: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 60: [----------] 15 tests from IndexBlockTest (0 ms total) 60: 60: [----------] 11 tests from IndexMapTest 60: [ RUN ] IndexMapTest.InitializesAtomBlock 60: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 60: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 60: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 60: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 60: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 60: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 60: [ RUN ] IndexMapTest.InitializesMoleculeBlock 60: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 60: [ RUN ] IndexMapTest.MapsSingleBlock 60: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 60: [ RUN ] IndexMapTest.MapsResidueBlocks 60: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 60: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 60: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 60: [ RUN ] IndexMapTest.HandlesMultipleRequests 60: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 60: [----------] 11 tests from IndexMapTest (0 ms total) 60: 60: [----------] 3 tests from IndexGroupsAndNamesTest 60: [ RUN ] IndexGroupsAndNamesTest.containsNames 60: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 60: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 60: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 60: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 60: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 60: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 60: 60: [----------] 15 tests from NeighborhoodSearchTest 60: [ RUN ] NeighborhoodSearchTest.SimpleSearch 60: [ OK ] NeighborhoodSearchTest.SimpleSearch (88 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 60: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (35 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchBox 60: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 60: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (28 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 60: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (30 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 60: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 60: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 60: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 60: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (165 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 60: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 60: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 60: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 60: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 60: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 60: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 60: [----------] 15 tests from NeighborhoodSearchTest (420 ms total) 60: 60: [----------] 13 tests from PositionCalculationTest 60: [ RUN ] PositionCalculationTest.ComputesAtomPositions 60: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 60: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 60: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 60: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 60: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 60: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 60: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 60: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionMask 60: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 60: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 60: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 60: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 60: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 60: [----------] 13 tests from PositionCalculationTest (1 ms total) 60: 60: [----------] 33 tests from SelectionCollectionTest 60: [ RUN ] SelectionCollectionTest.HandlesNoSelections 60: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 60: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 60: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 60: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 60: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 60: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 60: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 60: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (52 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 60: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 60: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 60: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 60: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 60: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (28 ms) 60: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 60: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 60: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 60: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 60: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 60: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 60: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 60: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 60: [----------] 33 tests from SelectionCollectionTest (87 ms total) 60: 60: [----------] 14 tests from SelectionCollectionInteractiveTest 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 60: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 60: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 60: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 60: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 60: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 60: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (32 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 60: [----------] 14 tests from SelectionCollectionInteractiveTest (35 ms total) 60: 60: [----------] 70 tests from SelectionCollectionDataTest 60: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 60: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 60: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResnr 60: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 60: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 60: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 60: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 60: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 60: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesChain 60: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMass 60: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesCharge 60: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 60: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 60: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (24 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 60: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBeta 60: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResname 60: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 60: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 60: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (20 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (14 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 60: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (0 ms) 60: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 60: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (20 ms) 60: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 60: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 60: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 60: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 60: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 60: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 60: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 60: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (20 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 60: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 60: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 60: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 60: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 60: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 60: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 60: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 60: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 60: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 60: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (20 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 60: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 60: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 60: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 60: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 60: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 60: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 60: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (16 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 60: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 60: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 60: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (20 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (21 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 60: [----------] 70 tests from SelectionCollectionDataTest (208 ms total) 60: 60: [----------] 17 tests from SelectionOptionTest 60: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 60: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 60: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 60: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 60: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksEmptySelections 60: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 60: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooManySelections 60: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 60: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 60: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesAdjuster 60: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 60: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 60: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (20 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 60: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 60: [----------] 17 tests from SelectionOptionTest (23 ms total) 60: 60: [----------] 9 tests from SelectionFileOptionTest 60: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 60: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 60: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 60: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 60: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 60: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 60: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 60: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 60: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 60: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 60: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 201 tests from 11 test suites ran. (785 ms total) 60: [ PASSED ] 201 tests. 60/87 Test #60: SelectionUnitTests ........................ Passed 0.90 sec test 61 Start 61: MdrunOutputTests 61: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunOutputTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 61: Test timeout computed to be: 600 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from MdrunTest 61: [ RUN ] MdrunTest.WritesHelp 61: [ OK ] MdrunTest.WritesHelp (59 ms) 61: [----------] 1 test from MdrunTest (59 ms total) 61: 61: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to 1557051879 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 21 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.079 0.040 199.7 61: (ns/day) (hour/ns) 61: Performance: 4.359 5.506 61: Reading frame 0 time 0.000 61: # Atoms 6 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (93 ms) 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to -276873217 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.048 0.024 199.4 61: (ns/day) (hour/ns) 61: Performance: 7.177 3.344 61: Reading frame 0 time 0.000 61: # Atoms 6 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (55 ms) 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to 1467874261 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 27 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.059 0.030 199.6 61: (ns/day) (hour/ns) 61: Performance: 5.832 4.115 61: Reading frame 0 time 0.000 61: # Atoms 3 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (64 ms) 61: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (214 ms total) 61: 61: [----------] 2 tests from Argon12/OutputFiles 61: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Number of degrees of freedom in T-Coupling group System is 33.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 68.810 K for 61: determining the Verlet buffer size 61: 61: 61: There were 3 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Argon' 61: 16 steps, 0.0 ps. 61: Generated 1 of the 1 non-bonded parameter combinations 61: 61: Excluding 1 bonded neighbours molecule type 'Argon' 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.343 0.172 199.9 61: (ns/day) (hour/ns) 61: Performance: 8.560 2.804 61: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (203 ms) 61: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Number of degrees of freedom in T-Coupling group System is 33.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 68.810 K for 61: determining the Verlet buffer size 61: 61: 61: There were 3 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Argon' 61: 16 steps, 0.0 ps. 61: Generated 1 of the 1 non-bonded parameter combinations 61: 61: Excluding 1 bonded neighbours molecule type 'Argon' 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 12 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.386 0.193 200.0 61: (ns/day) (hour/ns) 61: Performance: 7.610 3.154 61: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (210 ms) 61: [----------] 2 tests from Argon12/OutputFiles (414 ms total) 61: 61: [----------] 3 tests from MdrunCanWrite/Trajectories 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -74089523 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.194 0.097 199.9 61: (ns/day) (hour/ns) 61: Performance: 6.241 3.845 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (143 ms) 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -1081643139 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.183 0.091 199.9 61: (ns/day) (hour/ns) 61: Performance: 6.618 3.626 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (131 ms) 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -269551873 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.184 0.092 199.9 61: (ns/day) (hour/ns) 61: Performance: 6.575 3.650 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (134 ms) 61: [----------] 3 tests from MdrunCanWrite/Trajectories (410 ms total) 61: 61: [----------] 3 tests from MdrunCanWrite/NptTrajectories 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -1611169857 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 16 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.107 0.053 199.8 61: (ns/day) (hour/ns) 61: Performance: 4.855 4.943 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (88 ms) 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 61: The Berendsen barostat does not generate any strictly correct ensemble, 61: and should not be used for new production simulations (in our opinion). 61: We recommend using the C-rescale barostat instead. 61: 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: 61: There was 1 WARNING 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -287458313 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.147 0.074 199.8 61: (ns/day) (hour/ns) 61: Performance: 3.517 6.824 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (107 ms) 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 61: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -1111490601 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.017 0.009 198.7 61: (ns/day) (hour/ns) 61: Performance: 30.343 0.791 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (72 ms) 61: [----------] 3 tests from MdrunCanWrite/NptTrajectories (281 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (1500 ms total) 61: [ PASSED ] 12 tests. 61/87 Test #61: MdrunOutputTests .......................... Passed 1.60 sec test 62 Start 62: MdrunModulesTests 62: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunModulesTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 62: Test timeout computed to be: 600 62: [==========] Running 15 tests from 3 test suites. 62: [----------] Global test environment set-up. 62: [----------] 9 tests from DensityFittingTest 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -3.8565254e+03 62: Maximum force = 4.5099883e+03 on atom 3 62: Norm of force = 1.6816849e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1363741457 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (78 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -9.8207725e+03 62: Maximum force = 7.3954834e+03 on atom 2 62: Norm of force = 2.7825089e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1616385441 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (43 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (20 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Overriding nsteps with value passed on the command line: 4 steps 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 4 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 5 steps. 62: Potential Energy = -1.0954996e+04 62: Maximum force = 7.4724795e+03 on atom 2 62: Norm of force = 2.7758003e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -176849985 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (80 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (10 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -3.8565254e+03 62: Maximum force = 4.5099883e+03 on atom 3 62: Norm of force = 1.6816849e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -147884037 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (61 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -2.7138664e+04 62: Maximum force = 6.7827656e+03 on atom 2 62: Norm of force = 1.9608866e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to 2147159791 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (49 ms) 62: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: Setting the LD random seed to -67240449 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (37 ms) 62: [ RUN ] DensityFittingTest.CheckpointWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (2) 62: 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 62: NVE simulation: will use the initial temperature of 68.810 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Argon' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to -1630060714 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.093 0.046 199.8 62: (ns/day) (hour/ns) 62: Performance: 5.591 4.292 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Argon' 62: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.119 0.060 199.8 62: (ns/day) (hour/ns) 62: Performance: 7.227 3.321 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (147 ms) 62: [----------] 9 tests from DensityFittingTest (530 ms total) 62: 62: [----------] 4 tests from MimicTest 62: [ RUN ] MimicTest.OneQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 79 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.019 0.010 199.4 62: (ns/day) (hour/ns) 62: Performance: 9.015 2.662 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2080364511 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.OneQuantumMol (28 ms) 62: [ RUN ] MimicTest.AllQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 79 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.019 0.010 199.4 62: (ns/day) (hour/ns) 62: Performance: 8.879 2.703 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -906004485 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.AllQuantumMol (33 ms) 62: [ RUN ] MimicTest.TwoQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 25 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.014 0.007 199.3 62: (ns/day) (hour/ns) 62: Performance: 12.394 1.936 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -268468737 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.TwoQuantumMol (26 ms) 62: [ RUN ] MimicTest.BondCuts 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 66.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: NVE simulation: will use the initial temperature of 300.368 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 62: 62: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 36 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.009 0.005 199.0 62: (ns/day) (hour/ns) 62: Performance: 18.353 1.308 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -21895953 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.BondCuts (68 ms) 62: [----------] 4 tests from MimicTest (156 ms total) 62: 62: [----------] 2 tests from WithIntegrator/ImdTest 62: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 62: Generating 1-4 interactions: fudge = 1 62: 62: NOTE 1 [file glycine_vacuo.top, line 12]: 62: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 62: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 62: the time step of 2.0e-03 ps. 62: Maybe you forgot to change the constraints mdp option. 62: 62: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 62: Number of degrees of freedom in T-Coupling group System is 27.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: IMD: Enabled. This simulation will accept incoming IMD connections. 62: IMD: Pulling from IMD remote is enabled (-imdpull). 62: IMD: Setting port for connection requests to 0. 62: IMD: Setting up incoming socket. 62: IMD: Listening for IMD connection on port 39163. 62: IMD: -imdwait not set, starting simulation. 62: starting mdrun 'Glycine' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to -1241579717 62: 62: Generated 20503 of the 20503 non-bonded parameter combinations 62: 62: Generated 17396 of the 20503 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Glycine' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 13 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.111 0.056 199.8 62: (ns/day) (hour/ns) 62: Performance: 9.311 2.578 62: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (349 ms) 62: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 62: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 62: apply to steep. 62: 62: Generating 1-4 interactions: fudge = 1 62: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 62: Number of degrees of freedom in T-Coupling group System is 27.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: IMD: Enabled. This simulation will accept incoming IMD connections. 62: IMD: Pulling from IMD remote is enabled (-imdpull). 62: IMD: Setting port for connection requests to 0. 62: IMD: Setting up incoming socket. 62: IMD: Listening for IMD connection on port 55427. 62: IMD: -imdwait not set, starting simulation. 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = 1.1977061e+03 62: Maximum force = 1.7794875e+04 on atom 9 62: Norm of force = 7.8732895e+03 62: Setting the LD random seed to -1878595 62: 62: Generated 20503 of the 20503 non-bonded parameter combinations 62: 62: Generated 17396 of the 20503 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Glycine' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (313 ms) 62: [----------] 2 tests from WithIntegrator/ImdTest (663 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 15 tests from 3 test suites ran. (1444 ms total) 62: [ PASSED ] 15 tests. 62/87 Test #62: MdrunModulesTests ......................... Passed 1.53 sec test 63 Start 63: MdrunIOTests 63: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunIOTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 76 tests from 13 test suites. 63: [----------] Global test environment set-up. 63: [----------] 9 tests from GromppTest 63: [ RUN ] GromppTest.EmptyMdpFileWorks 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -29513769 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.EmptyMdpFileWorks (23 ms) 63: [ RUN ] GromppTest.SimulatedAnnealingWorks 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Simulated annealing for group rest: Periodic, 4 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 2.0 320.0 63: 4.0 320.0 63: 6.0 298.0 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -403376167 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.SimulatedAnnealingWorks (22 ms) 63: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Simulated annealing for group Methanol: Single, 3 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 3.0 280.0 63: 6.0- 270.0 63: Simulated annealing for group SOL: Periodic, 4 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 2.0 320.0 63: 4.0 320.0 63: 6.0 298.0 63: Number of degrees of freedom in T-Coupling group Methanol is 7.20 63: Number of degrees of freedom in T-Coupling group SOL is 4.80 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -4786714 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 63: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 63: Setting the LD random seed to -536874253 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (48 ms) 63: [ RUN ] GromppTest.HandlesMaxwarn 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: The Berendsen thermostat does not generate the correct kinetic energy 63: distribution, and should not be used for new production simulations (in 63: our opinion). We would recommend the V-rescale thermostat. 63: 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: 63: There was 1 WARNING 63: Setting the LD random seed to -75637006 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 63: [ RUN ] GromppTest.MaxwarnShouldBePositive 63: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 63: [ RUN ] GromppTest.ValidTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Pull group 1 'SOL' has 3 atoms 63: Pull group 2 'Methanol' has 3 atoms 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -20529 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.ValidTransformationCoord (15 ms) 63: [ RUN ] GromppTest.InvalidTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Pull group 1 'SOL' has 3 atoms 63: Pull group 2 'Methanol' has 3 atoms 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 1 3 5 63: 2 3 2 Setting the LD random seed to 499515385 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: [ OK ] GromppTest.InvalidTransformationCoord (23 ms) 63: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 63: Setting the LD random seed to 1845450685 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (25 ms) 63: [----------] 9 tests from GromppTest (165 ms total) 63: 63: [----------] 6 tests from MdrunTerminationTest 63: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -1619429961 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.078 0.039 199.7 63: (ns/day) (hour/ns) 63: Performance: 6.602 3.635 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.050 0.025 199.5 63: (ns/day) (hour/ns) 63: Performance: 10.291 2.332 63: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (147 ms) 63: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 1, rlist from 1.032 to 1 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 100 steps, 0.1 ps. 63: 63: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 63: Setting the LD random seed to -6377745 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: NOTE: 25 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.066 0.033 199.5 63: (ns/day) (hour/ns) 63: Performance: 5.198 4.617 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 102 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 100 63: Runtime for the run 0.1 ps 63: Run end step 100 63: Run end time 0.1 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 102 63: Runtime for the run 0.102 ps 63: Run end step 102 63: Run end time 0.102 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.600 0.800 200.0 63: (ns/day) (hour/ns) 63: Performance: 11.017 2.178 63: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (869 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -100926881 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 19 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.079 0.040 199.7 63: (ns/day) (hour/ns) 63: Performance: 6.534 3.673 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.073 0.036 199.8 63: (ns/day) (hour/ns) 63: Performance: 7.112 3.375 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 6 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 6 63: Runtime for the run 0.006 ps 63: Run end step 6 63: Run end time 0.006 ps 63: 63: 63: Writing final coordinates. 63: 63: NOTE: 44 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.055 0.028 199.7 63: (ns/day) (hour/ns) 63: Performance: 9.390 2.556 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 8 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 6 63: Runtime for the run 0.006 ps 63: Run end step 6 63: Run end time 0.006 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 8 63: Runtime for the run 0.008 ps 63: Run end step 8 63: Run end time 0.008 ps 63: 63: 63: Writing final coordinates. 63: 63: NOTE: 19 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.086 0.043 199.8 63: (ns/day) (hour/ns) 63: Performance: 6.021 3.986 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: NOTE: 58 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.041 0.020 199.6 63: (ns/day) (hour/ns) 63: Performance: 4.252 5.644 63: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (248 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -270925831 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 28 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.080 0.040 199.7 63: (ns/day) (hour/ns) 63: Performance: 6.442 3.725 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps. 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.116 0.058 199.8 63: (ns/day) (hour/ns) 63: Performance: 7.456 3.219 63: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (147 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to 2078662655 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 24 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.077 0.039 199.7 63: (ns/day) (hour/ns) 63: Performance: 6.696 3.584 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (64 ms) 63: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -1073874956 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.097 0.049 199.7 63: (ns/day) (hour/ns) 63: Performance: 5.337 4.497 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Setting nsteps to 4 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: NOTE: 19 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.070 0.035 199.7 63: (ns/day) (hour/ns) 63: Performance: 7.357 3.262 63: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (120 ms) 63: [----------] 6 tests from MdrunTerminationTest (1610 ms total) 63: 63: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 63: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.372 0.186 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.897 3.039 63: trr version: GMX_trn_file (single precision) 63: 63: 63: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (216 ms) 63: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.446 0.223 200.0 63: (ns/day) (hour/ns) 63: Performance: 6.585 3.644 63: 63: 63: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (244 ms) 63: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (461 ms total) 63: 63: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.278 0.139 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.578 2.269 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.135 0.068 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.501 2.087 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.153 0.077 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.135 2.368 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (336 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.262 0.131 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.214 2.140 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.101 0.050 199.7 63: (ns/day) (hour/ns) 63: Performance: 15.447 1.554 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.103 0.052 199.8 63: (ns/day) (hour/ns) 63: Performance: 15.026 1.597 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (274 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.195 0.098 199.9 63: (ns/day) (hour/ns) 63: Performance: 15.061 1.593 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 16 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.129 0.064 199.9 63: (ns/day) (hour/ns) 63: Performance: 12.082 1.986 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.106 0.053 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.608 1.643 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (259 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.218 0.109 199.9 63: (ns/day) (hour/ns) 63: Performance: 13.493 1.779 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 15 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.111 0.056 199.9 63: (ns/day) (hour/ns) 63: Performance: 13.976 1.717 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.111 0.056 199.8 63: (ns/day) (hour/ns) 63: Performance: 13.983 1.716 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (260 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.184 0.092 199.9 63: (ns/day) (hour/ns) 63: Performance: 15.929 1.507 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.139 0.070 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.166 2.149 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 24 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.146 0.073 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.659 2.252 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (273 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.235 0.118 199.9 63: (ns/day) (hour/ns) 63: Performance: 12.499 1.920 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 18 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.133 0.066 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.700 2.051 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.133 0.066 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.702 2.051 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (297 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.195 0.097 199.9 63: (ns/day) (hour/ns) 63: Performance: 15.068 1.593 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 18 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.105 0.053 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.799 1.622 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 18 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.123 0.062 199.8 63: (ns/day) (hour/ns) 63: Performance: 12.591 1.906 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (254 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.234 0.117 199.9 63: (ns/day) (hour/ns) 63: Performance: 12.572 1.909 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.138 0.069 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.236 2.136 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.184 0.092 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.439 2.844 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (319 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.312 0.156 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.425 2.546 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.163 0.082 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.525 2.520 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.168 0.084 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.268 2.589 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (386 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.298 0.149 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.866 2.432 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.165 0.082 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.436 2.543 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.168 0.084 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.230 2.600 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (367 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.399 0.199 200.0 63: (ns/day) (hour/ns) 63: Performance: 7.364 3.259 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.207 0.103 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.513 3.194 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.200 0.100 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.783 3.084 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (441 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.362 0.181 200.0 63: (ns/day) (hour/ns) 63: Performance: 8.115 2.957 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.212 0.106 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.320 3.278 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.202 0.101 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.700 3.117 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (431 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.314 0.157 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.357 2.565 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.159 0.079 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.796 2.450 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.194 0.097 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.004 2.999 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (400 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.378 0.189 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.771 3.088 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.206 0.103 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.531 3.187 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.258 0.129 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.021 3.986 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (495 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.469 0.234 200.0 63: (ns/day) (hour/ns) 63: Performance: 6.265 3.831 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.238 0.119 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.545 3.667 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.259 0.129 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.005 3.997 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (568 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.443 0.222 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.624 3.623 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.246 0.123 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.330 3.791 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.250 0.125 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.211 3.864 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (546 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.276 0.638 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.302 10.425 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.526 0.263 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.957 8.115 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.555 0.278 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.800 8.572 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (1413 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.219 0.109 199.9 63: (ns/day) (hour/ns) 63: Performance: 13.434 1.787 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.777 0.389 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.002 11.991 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.777 0.388 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.002 11.989 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (1139 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.227 0.614 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.393 10.030 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.795 0.398 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.955 12.276 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.879 0.440 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.768 13.575 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (1669 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.592 0.796 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.845 13.008 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.841 0.421 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.848 12.988 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.714 0.357 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.176 11.027 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (1811 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.216 0.608 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.415 9.936 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.071 0.036 199.6 63: (ns/day) (hour/ns) 63: Performance: 21.727 1.105 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.080 0.040 199.6 63: (ns/day) (hour/ns) 63: Performance: 19.453 1.234 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (972 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.388 0.694 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.116 11.343 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.696 0.348 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.236 10.735 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.682 0.341 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.278 10.534 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (2061 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.776 0.888 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.654 14.507 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.988 0.494 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.574 15.252 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.008 0.504 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.543 15.559 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (2143 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.579 0.790 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.860 12.903 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.868 0.434 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.791 13.399 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.905 0.452 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.719 13.965 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (1993 ms) 63: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (19121 ms total) 63: 63: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.529 0.265 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.553 4.322 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.336 0.168 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.626 5.189 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.278 0.139 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.584 4.298 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (722 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.518 0.259 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.673 4.231 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.443 0.221 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.513 6.833 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.361 0.180 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.309 5.569 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (846 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.735 0.368 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.994 6.008 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.471 0.236 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.299 7.274 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.541 0.271 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.871 8.359 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1023 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.635 0.318 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.625 5.189 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.226 0.113 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.883 3.487 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.208 0.104 199.8 63: (ns/day) (hour/ns) 63: Performance: 7.467 3.214 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (703 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.387 0.193 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.597 3.159 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.230 0.115 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.754 3.553 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.212 0.106 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.343 3.269 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (531 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.402 0.201 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.314 3.281 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.343 0.172 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.529 5.299 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.367 0.184 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.234 5.668 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (988 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.026 0.513 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.864 8.381 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.703 0.352 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.211 10.855 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.726 0.363 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.141 11.211 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (1499 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.226 0.613 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.396 10.015 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.671 0.336 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.316 10.361 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.535 0.268 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.906 8.260 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1617 ms) 63: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (7931 ms total) 63: 63: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.400 0.200 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.336 3.271 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.211 0.106 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.355 3.263 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.210 0.105 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.397 3.245 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (505 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.359 0.180 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.180 2.934 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.186 0.093 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.376 2.865 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.177 0.088 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.791 2.730 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (442 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.321 0.160 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.154 2.622 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.283 0.142 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.488 4.373 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 37 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.121 0.061 199.8 63: (ns/day) (hour/ns) 63: Performance: 12.804 1.874 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (436 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.140 0.070 199.8 63: (ns/day) (hour/ns) 63: Performance: 20.981 1.144 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.201 0.101 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.737 3.102 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.261 0.130 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.966 4.023 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (345 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.592 0.296 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.960 4.839 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.328 0.164 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.740 5.063 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 15 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.321 0.161 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.842 4.956 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (725 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.574 0.287 200.0 63: (ns/day) (hour/ns) 63: Performance: 5.117 4.690 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.400 0.200 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.886 6.176 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.382 0.191 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.070 5.897 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (784 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.833 0.417 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.526 6.806 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.471 0.236 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.302 7.269 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.448 0.224 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.471 6.915 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (1000 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.608 0.304 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.830 4.969 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.230 0.115 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.761 3.550 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.219 0.110 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.090 3.385 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (645 ms) 63: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (4885 ms total) 63: 63: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 63: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.338 0.169 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.695 2.760 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.193 0.096 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.061 2.977 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.200 0.100 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.772 3.088 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (430 ms) 63: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.306 0.153 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.603 2.499 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.154 0.077 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.063 2.385 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.187 0.094 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.295 2.893 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (371 ms) 63: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (802 ms total) 63: 63: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.202 0.101 199.9 63: (ns/day) (hour/ns) 63: Performance: 14.558 1.649 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.108 0.054 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.328 1.675 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.109 0.055 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.242 1.685 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (246 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.206 0.103 199.9 63: (ns/day) (hour/ns) 63: Performance: 14.264 1.683 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 29 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.117 0.058 199.8 63: (ns/day) (hour/ns) 63: Performance: 13.294 1.805 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.110 0.055 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.137 1.698 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (251 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.160 0.080 199.8 63: (ns/day) (hour/ns) 63: Performance: 18.388 1.305 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.100 0.050 199.7 63: (ns/day) (hour/ns) 63: Performance: 15.504 1.548 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.073 0.037 199.6 63: (ns/day) (hour/ns) 63: Performance: 21.243 1.130 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (196 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.129 0.064 199.8 63: (ns/day) (hour/ns) 63: Performance: 22.799 1.053 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.071 0.036 199.7 63: (ns/day) (hour/ns) 63: Performance: 21.891 1.096 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.066 0.033 199.6 63: (ns/day) (hour/ns) 63: Performance: 23.356 1.028 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (153 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.385 0.192 200.0 63: (ns/day) (hour/ns) 63: Performance: 7.632 3.145 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.258 0.129 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.036 3.976 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.248 0.124 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.263 3.832 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (485 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.442 0.221 200.0 63: (ns/day) (hour/ns) 63: Performance: 6.647 3.610 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.132 0.066 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.812 2.032 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.140 0.070 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.136 2.155 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (425 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.279 0.140 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.517 2.282 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.139 0.069 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.199 2.143 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.171 0.085 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.107 2.635 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (339 ms) 63: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (2098 ms total) 63: 63: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 63: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.409 0.204 200.0 63: (ns/day) (hour/ns) 63: Performance: 7.186 3.340 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.213 0.106 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.312 3.282 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.302 0.151 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.147 4.663 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (500 ms) 63: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (500 ms total) 63: 63: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 63: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.269 0.134 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.922 2.197 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.154 0.077 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.112 2.374 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.159 0.079 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.798 2.450 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (353 ms) 63: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.442 0.221 200.0 63: (ns/day) (hour/ns) 63: Performance: 6.639 3.615 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.192 0.096 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.111 2.959 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.196 0.098 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.917 3.032 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (470 ms) 63: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (824 ms total) 63: 63: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 63: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: Setting the AWH bias MC random seed to -540033814 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Setting the AWH bias MC random seed to 2004612095 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.480 0.240 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.115 3.925 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.259 0.130 199.8 63: (ns/day) (hour/ns) 63: Performance: 5.989 4.007 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.273 0.136 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.701 4.210 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (698 ms) 63: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: Setting the AWH bias MC random seed to -2019574803 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Setting the AWH bias MC random seed to 1072684411 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.299 0.150 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.820 2.444 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.192 0.096 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.111 2.959 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.231 0.116 199.8 63: (ns/day) (hour/ns) 63: Performance: 6.726 3.568 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (537 ms) 63: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (1236 ms total) 63: 63: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 63: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.498 0.249 200.0 63: (ns/day) (hour/ns) 63: Performance: 5.900 4.068 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.375 0.188 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.143 5.792 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.603 0.301 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.579 9.305 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (851 ms) 63: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (851 ms total) 63: 63: [----------] 3 tests from Checking/InitialConstraintsTest 63: [ RUN ] Checking/InitialConstraintsTest.Works/0 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -407507213 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 23 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.101 0.050 199.7 63: (ns/day) (hour/ns) 63: Performance: 3.424 7.009 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (142 ms) 63: [ RUN ] Checking/InitialConstraintsTest.Works/1 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -402653187 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.165 0.083 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.094 11.459 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (129 ms) 63: [ RUN ] Checking/InitialConstraintsTest.Works/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: Integrator method md-vv-avek is implemented primarily for validation 63: purposes; for molecular dynamics, you should probably be using md or 63: md-vv 63: 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -1483266 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.092 0.046 199.7 63: (ns/day) (hour/ns) 63: Performance: 3.754 6.394 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (112 ms) 63: [----------] 3 tests from Checking/InitialConstraintsTest (384 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 76 tests from 13 test suites ran. (41214 ms total) 63: [ PASSED ] 76 tests. 63/87 Test #63: MdrunIOTests .............................. Passed 41.28 sec test 64 Start 64: MdrunTestsOneRank 64: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunTestsOneRank.xml" 64: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 28 tests from 7 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from CompelTest 64: [ RUN ] CompelTest.SwapCanRun 64: Generating 1-4 interactions: fudge = 0.5 64: Split0 group 'Ch0' contains 83 atoms. 64: Split1 group 'Ch1' contains 83 atoms. 64: Solvent group 'SOL' contains 11931 atoms. 64: Swap group 'NA+' contains 19 atoms. 64: Swap group 'CL-' contains 19 atoms. 64: Number of degrees of freedom in T-Coupling group System is 27869.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 64: Removing center of mass motion in the presence of position restraints 64: might cause artifacts. When you are using position restraints to 64: equilibrate a macro-molecule, the artifacts are usually negligible. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Update groups can not be used for this system because there are three or more consecutively coupled constraints 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: SWAP: Determining initial numbers of ions per compartment. 64: SWAP: Setting pointers for checkpoint writing 64: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 64: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 64: starting mdrun 'Channel_coco in octane membrane' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -570703877 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein' 64: 64: turning all bonds into constraints... 64: 64: Excluding 3 bonded neighbours molecule type 'OCT' 64: 64: turning all bonds into constraints... 64: 64: Excluding 1 bonded neighbours molecule type 'NA' 64: 64: turning all bonds into constraints... 64: 64: Excluding 1 bonded neighbours molecule type 'CL' 64: 64: turning all bonds into constraints... 64: 64: Excluding 3 bonded neighbours molecule type 'Protein' 64: 64: Excluding 3 bonded neighbours molecule type 'OCT' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning all bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 1 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 28 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 1.080 0.540 200.0 64: (ns/day) (hour/ns) 64: Performance: 2.399 10.002 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 64: 64: Update groups can not be used for this system because there are three or more consecutively coupled constraints 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: SWAP: Setting pointers for checkpoint writing 64: SWAP: Copying channel fluxes from checkpoint file data 64: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 64: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 64: starting mdrun 'Channel_coco in octane membrane' 64: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 64: 64: Writing final coordinates. 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.818 0.409 200.0 64: (ns/day) (hour/ns) 64: Performance: 3.167 7.578 64: [ OK ] CompelTest.SwapCanRun (2119 ms) 64: [----------] 1 test from CompelTest (2119 ms total) 64: 64: [----------] 6 tests from BondedInteractionsTest 64: [ RUN ] BondedInteractionsTest.NormalBondWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 2 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 21 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.016 0.008 199.3 64: (ns/day) (hour/ns) 64: Performance: 10.704 2.242 64: Setting the LD random seed to 2077089239 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalBondWorks (39 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 2 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 22 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.036 0.018 199.7 64: (ns/day) (hour/ns) 64: Performance: 4.746 5.057 64: Setting the LD random seed to -425390338 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedBondWorks (44 ms) 64: [ RUN ] BondedInteractionsTest.NormalAngleWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 38 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.045 0.022 199.8 64: (ns/day) (hour/ns) 64: Performance: 3.848 6.236 64: Setting the LD random seed to -104874177 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalAngleWorks (40 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 10 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.032 0.016 199.6 64: (ns/day) (hour/ns) 64: Performance: 5.364 4.474 64: Setting the LD random seed to -169951331 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (32 ms) 64: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.037 0.018 199.7 64: (ns/day) (hour/ns) 64: Performance: 4.687 5.121 64: Setting the LD random seed to -60832003 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalDihedralWorks (39 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 58 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.029 0.015 199.6 64: (ns/day) (hour/ns) 64: Performance: 5.944 4.038 64: Setting the LD random seed to -281645637 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (30 ms) 64: [----------] 6 tests from BondedInteractionsTest (226 ms total) 64: 64: [----------] 2 tests from BoxDeformationTest 64: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (10) 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 0 steps, 0.0 ps. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.038 0.019 199.4 64: (ns/day) (hour/ns) 64: Performance: 9.181 2.614 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1612811283 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Setting gen_seed to -470098465 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (62 ms) 64: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (10) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 1293.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 20 steps, 0.0 ps. 64: Setting the LD random seed to -25331841 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 64: 64: Estimate for the relative computational load of the PME mesh part: 0.23 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 1.162 0.581 200.0 64: (ns/day) (hour/ns) 64: Performance: 6.245 3.843 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (7357 ms) 64: [----------] 2 tests from BoxDeformationTest (7420 ms total) 64: 64: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -65016009 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.95 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.279 0.140 199.9 64: (ns/day) (hour/ns) 64: Performance: 3.093 7.760 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 2109530111 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.95 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.249 0.125 199.9 64: (ns/day) (hour/ns) 64: Performance: 3.469 6.918 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 64: 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (111680 ms) 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -763363333 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.95 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.271 0.136 199.9 64: (ns/day) (hour/ns) 64: Performance: 3.184 7.538 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 737935339 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.95 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.250 0.125 199.9 64: (ns/day) (hour/ns) 64: Performance: 3.458 6.940 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (425 ms) 64: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (112105 ms total) 64: 64: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Pull group 1 'FirstWaterMolecule' has 3 atoms 64: Pull group 2 'SecondWaterMolecule' has 3 atoms 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Pull group natoms pbc atom distance at start reference at t=0 64: 1 3 2 64: 2 3 5 1.112 nm 1.000 nm 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 1488777086 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.118 0.059 199.8 64: (ns/day) (hour/ns) 64: Performance: 7.333 3.273 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Pull group 1 'FirstWaterMolecule' has 3 atoms 64: Pull group 2 'SecondWaterMolecule' has 3 atoms 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Pull group natoms pbc atom distance at start reference at t=0 64: 1 3 2 64: 2 3 5 1.112 nm 1.000 nm 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 1711108094 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.165 0.083 199.8 64: (ns/day) (hour/ns) 64: Performance: 5.216 4.601 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (227 ms) 64: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (227 ms total) 64: 64: [----------] 12 tests from FreezeWorks/FreezeGroupTest 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 11 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.280 0.140 199.9 64: (ns/day) (hour/ns) 64: Performance: 5.557 4.319 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (207 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.265 0.132 199.9 64: (ns/day) (hour/ns) 64: Performance: 5.869 4.089 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (186 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.256 0.128 199.9 64: (ns/day) (hour/ns) 64: Performance: 6.071 3.953 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (193 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.352 0.176 199.9 64: (ns/day) (hour/ns) 64: Performance: 4.415 5.436 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (235 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.283 0.142 199.9 64: (ns/day) (hour/ns) 64: Performance: 5.490 4.372 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (189 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 64: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 64: Parrinello-Rahman is not implemented in md-vv. 64: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.259 0.129 199.9 64: (ns/day) (hour/ns) 64: Performance: 6.012 3.992 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (186 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.284 0.142 199.9 64: (ns/day) (hour/ns) 64: Performance: 5.475 4.383 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (196 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.189 0.094 199.9 64: (ns/day) (hour/ns) 64: Performance: 8.237 2.914 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (143 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.149 0.075 199.8 64: (ns/day) (hour/ns) 64: Performance: 10.437 2.299 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (149 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.150 0.075 199.8 64: (ns/day) (hour/ns) 64: Performance: 10.392 2.309 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (154 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.180 0.090 199.8 64: (ns/day) (hour/ns) 64: Performance: 8.648 2.775 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (171 ms) 64: [----------] 12 tests from FreezeWorks/FreezeGroupTest (2015 ms total) 64: 64: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -262917 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 19 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.137 0.069 199.8 64: (ns/day) (hour/ns) 64: Performance: 22.679 1.058 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (92 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because verlet-buffer-tolerance is not set or used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to 2000158438 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 18 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.136 0.068 199.8 64: (ns/day) (hour/ns) 64: Performance: 22.923 1.047 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (95 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -622332931 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.195 0.097 199.9 64: (ns/day) (hour/ns) 64: Performance: 15.978 1.502 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (120 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because verlet-buffer-tolerance is not set or used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to 1476373391 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.153 0.076 199.8 64: (ns/day) (hour/ns) 64: Performance: 20.339 1.180 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (91 ms) 64: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (400 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 28 tests from 7 test suites ran. (124715 ms total) 64: [ PASSED ] 27 tests. 64: [ SKIPPED ] 1 test, listed below: 64: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 64/87 Test #64: MdrunTestsOneRank ......................... Passed 124.77 sec test 65 Start 65: MdrunTestsTwoRanks 65: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunTestsTwoRanks.xml" 65: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 28 tests from 7 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from CompelTest 65: [ RUN ] CompelTest.SwapCanRun 65: Generating 1-4 interactions: fudge = 0.5 65: Split0 group 'Ch0' contains 83 atoms. 65: Split1 group 'Ch1' contains 83 atoms. 65: Solvent group 'SOL' contains 11931 atoms. 65: Swap group 'NA+' contains 19 atoms. 65: Swap group 'CL-' contains 19 atoms. 65: Number of degrees of freedom in T-Coupling group System is 27869.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 65: Removing center of mass motion in the presence of position restraints 65: might cause artifacts. When you are using position restraints to 65: equilibrate a macro-molecule, the artifacts are usually negligible. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because there are three or more consecutively coupled constraints 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: SWAP: Determining initial numbers of ions per compartment. 65: SWAP: Setting pointers for checkpoint writing 65: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 65: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 65: starting mdrun 'Channel_coco in octane membrane' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to 724258239 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein' 65: 65: turning all bonds into constraints... 65: 65: Excluding 3 bonded neighbours molecule type 'OCT' 65: 65: turning all bonds into constraints... 65: 65: Excluding 1 bonded neighbours molecule type 'NA' 65: 65: turning all bonds into constraints... 65: 65: Excluding 1 bonded neighbours molecule type 'CL' 65: 65: turning all bonds into constraints... 65: 65: Excluding 3 bonded neighbours molecule type 'Protein' 65: 65: Excluding 3 bonded neighbours molecule type 'OCT' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning all bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 1 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 0.8%. 65: The balanceable part of the MD step is 11%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.1%. 65: 65: 65: NOTE: 38 % of the run time was spent in domain decomposition, 65: 6 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 7.112 1.820 390.8 65: (ns/day) (hour/ns) 65: Performance: 0.712 33.703 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 65: 65: Update groups can not be used for this system because there are three or more consecutively coupled constraints 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: SWAP: Setting pointers for checkpoint writing 65: SWAP: Copying channel fluxes from checkpoint file data 65: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 65: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 65: starting mdrun 'Channel_coco in octane membrane' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.024 0.756 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.714 14.001 65: [ OK ] CompelTest.SwapCanRun (5885 ms) 65: [----------] 1 test from CompelTest (5885 ms total) 65: 65: [----------] 6 tests from BondedInteractionsTest 65: [ RUN ] BondedInteractionsTest.NormalBondWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 2 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 70 % of the run time was spent in domain decomposition, 65: 3 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 9 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.835 0.209 399.9 65: (ns/day) (hour/ns) 65: Performance: 0.414 57.980 65: Setting the LD random seed to -155417634 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalBondWorks (1316 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 2 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 66 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.413 0.103 399.9 65: (ns/day) (hour/ns) 65: Performance: 0.837 28.689 65: Setting the LD random seed to -1208503337 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedBondWorks (915 ms) 65: [ RUN ] BondedInteractionsTest.NormalAngleWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 87 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.972 0.789 376.7 65: (ns/day) (hour/ns) 65: Performance: 0.110 219.146 65: Setting the LD random seed to -1229006082 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalAngleWorks (2692 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 65 % of the run time was spent in domain decomposition, 65: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.217 0.054 399.8 65: (ns/day) (hour/ns) 65: Performance: 1.591 15.088 65: Setting the LD random seed to -807029073 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (615 ms) 65: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 79 % of the run time was spent in domain decomposition, 65: 3 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.397 0.372 376.0 65: (ns/day) (hour/ns) 65: Performance: 0.232 103.231 65: Setting the LD random seed to -575537221 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalDihedralWorks (937 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 66 % of the run time was spent in domain decomposition, 65: 11 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.380 0.095 399.9 65: (ns/day) (hour/ns) 65: Performance: 0.910 26.368 65: Setting the LD random seed to -552869889 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (366 ms) 65: [----------] 6 tests from BondedInteractionsTest (6844 ms total) 65: 65: [----------] 2 tests from BoxDeformationTest 65: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (10) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 0 steps, 0.0 ps. 65: 65: NOTE: 49 % of the run time was spent in domain decomposition, 65: 16 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.237 0.094 252.4 65: (ns/day) (hour/ns) 65: Performance: 1.843 13.020 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -388017225 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Setting gen_seed to 972542639 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (436 ms) 65: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (10) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 1293.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 20 steps, 0.0 ps. 65: Setting the LD random seed to -1092354947 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 65: 65: Estimate for the relative computational load of the PME mesh part: 0.23 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 4.7%. 65: The balanceable part of the MD step is 13%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.6%. 65: 65: 65: NOTE: 11 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 22.896 5.768 397.0 65: (ns/day) (hour/ns) 65: Performance: 0.629 38.148 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (13143 ms) 65: [----------] 2 tests from BoxDeformationTest (13580 ms total) 65: 65: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 947300339 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.95 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 8 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.720 1.230 383.8 65: (ns/day) (hour/ns) 65: Performance: 0.351 68.332 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 1945843134 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.95 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 8 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.280 1.126 380.1 65: (ns/day) (hour/ns) 65: Performance: 0.384 62.554 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 65: 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (137096 ms) 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 2122727419 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.95 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 8 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.912 1.266 387.9 65: (ns/day) (hour/ns) 65: Performance: 0.341 70.353 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -1227490307 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.95 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 17 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.184 0.813 391.9 65: (ns/day) (hour/ns) 65: Performance: 0.532 45.140 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (5072 ms) 65: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (142181 ms total) 65: 65: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 805303285 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 11 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.359 0.626 377.0 65: (ns/day) (hour/ns) 65: Performance: 0.691 34.755 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 1610390255 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 16 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.664 0.416 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.038 23.118 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (1952 ms) 65: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (1952 ms total) 65: 65: [----------] 12 tests from FreezeWorks/FreezeGroupTest 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 41.5%. 65: The balanceable part of the MD step is 37%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 15.3%. 65: 65: NOTE: 15.3 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 20 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 13 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.726 0.979 380.5 65: (ns/day) (hour/ns) 65: Performance: 0.794 30.220 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (2157 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 31.8%. 65: The balanceable part of the MD step is 37%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 11.8%. 65: 65: NOTE: 11.8 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 20 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.168 0.805 393.8 65: (ns/day) (hour/ns) 65: Performance: 0.967 24.831 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (1210 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 36.7%. 65: The balanceable part of the MD step is 33%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 12.1%. 65: 65: NOTE: 12.1 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 28 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 5 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.059 1.023 396.8 65: (ns/day) (hour/ns) 65: Performance: 0.760 31.570 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (1968 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 23.0%. 65: The balanceable part of the MD step is 34%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 7.8%. 65: 65: NOTE: 7.8 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 24 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 23 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.269 1.113 383.5 65: (ns/day) (hour/ns) 65: Performance: 0.699 34.357 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (2203 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 22.8%. 65: The balanceable part of the MD step is 49%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 11.1%. 65: 65: NOTE: 11.1 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 16 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 20 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.535 1.155 392.6 65: (ns/day) (hour/ns) 65: Performance: 0.673 35.648 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (1687 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 65: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 65: Parrinello-Rahman is not implemented in md-vv. 65: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 19 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.079 0.541 384.1 65: (ns/day) (hour/ns) 65: Performance: 1.436 16.707 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (983 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 10 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 14 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.842 0.992 387.3 65: (ns/day) (hour/ns) 65: Performance: 0.784 30.622 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (2608 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 13 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 12 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.932 0.733 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.060 22.632 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (1241 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.640 0.668 395.2 65: (ns/day) (hour/ns) 65: Performance: 1.164 20.618 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (1397 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 21 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.963 0.778 380.9 65: (ns/day) (hour/ns) 65: Performance: 1.000 24.011 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (1440 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 14 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 13 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.730 0.728 375.0 65: (ns/day) (hour/ns) 65: Performance: 1.068 22.469 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (1975 ms) 65: [----------] 12 tests from FreezeWorks/FreezeGroupTest (18876 ms total) 65: 65: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -109746247 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 4.1%. 65: The balanceable part of the MD step is 41%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 1.7%. 65: 65: 65: NOTE: 20 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 11 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.320 0.858 387.0 65: (ns/day) (hour/ns) 65: Performance: 1.813 13.240 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (1388 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because verlet-buffer-tolerance is not set or used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -88080385 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 7.1%. 65: The balanceable part of the MD step is 37%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 2.6%. 65: 65: 65: NOTE: 14 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 18 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.832 0.708 399.9 65: (ns/day) (hour/ns) 65: Performance: 2.196 10.928 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (1352 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to 1004445177 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 2.1%. 65: The balanceable part of the MD step is 41%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.9%. 65: 65: 65: NOTE: 16 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 24 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 5.784 1.484 389.8 65: (ns/day) (hour/ns) 65: Performance: 1.048 22.900 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (3316 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because verlet-buffer-tolerance is not set or used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -134292033 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 2.1%. 65: The balanceable part of the MD step is 41%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.9%. 65: 65: 65: NOTE: 17 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 23 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 5.768 1.494 386.1 65: (ns/day) (hour/ns) 65: Performance: 1.041 23.055 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (3340 ms) 65: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (9417 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 28 tests from 7 test suites ran. (198938 ms total) 65: [ PASSED ] 27 tests. 65: [ SKIPPED ] 1 test, listed below: 65: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 65/87 Test #65: MdrunTestsTwoRanks ........................ Passed 198.98 sec test 66 Start 66: MdrunSingleRankAlgorithmsTests 66: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 5 tests from 3 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from DispersionCorrectionTest 66: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 30.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 200 steps, 0.4 ps. 66: Setting the LD random seed to 943649661 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning H bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Converted 3 Bonds with virtual sites to connections, 7 left 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 12 Constraints with virtual sites to connections, 0 left 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 8.528 4.264 200.0 66: (ns/day) (hour/ns) 66: Performance: 8.145 2.946 66: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (4440 ms) 66: [----------] 1 test from DispersionCorrectionTest (4440 ms total) 66: 66: [----------] 1 test from OriresTest 66: [ RUN ] OriresTest.OriresCanRun 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 518.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 66: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 66: 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 66: 10 steps, 0.0 ps. 66: Setting the LD random seed to 511625085 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.273 0.137 199.9 66: (ns/day) (hour/ns) 66: Performance: 13.914 1.725 66: [ OK ] OriresTest.OriresCanRun (1455 ms) 66: [----------] 1 test from OriresTest (1455 ms total) 66: 66: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 66: Number of degrees of freedom in T-Coupling group rest is 10.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Dipoles' 66: 20 steps, 0.1 ps. 66: Setting the LD random seed to -1210444498 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Dipole' 66: 66: Searching the wall atom type(s) 66: 66: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 66: 66: Estimate for the relative computational load of the PME mesh part: 1.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 1.221 0.610 200.0 66: (ns/day) (hour/ns) 66: Performance: 7.431 3.230 66: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 66: 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (225939 ms) 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 66: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 66: The supported numbers are > 1. 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: With epsilon_surface > 0 all molecules should be neutral. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: With epsilon_surface > 0 you can only use domain decomposition when there 66: are only small molecules with all bonds constrained (mdrun will check for 66: this). 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Dipoles' 66: 20 steps, 0.1 ps. 66: Setting the LD random seed to -7434251 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Dipole' 66: 66: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 66: 66: Estimate for the relative computational load of the PME mesh part: 1.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.914 0.457 200.0 66: (ns/day) (hour/ns) 66: Performance: 9.923 2.419 66: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (93005 ms) 66: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (318945 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 5 tests from 3 test suites ran. (324942 ms total) 66: [ PASSED ] 5 tests. 66/87 Test #66: MdrunSingleRankAlgorithmsTests ............ Passed 325.01 sec test 67 Start 67: Minimize1RankTests 67: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Minimize1RankTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 12 tests from 2 test suites. 67: [----------] Global test environment set-up. 67: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -4.7990997e+01 67: Maximum force = 1.8629692e+02 on atom 13 67: Norm of force = 8.7721836e+01 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (786 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 3.02331e+02 on atom 3 67: F-Norm = 1.18024e+02 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -5.5862350e+01 67: Maximum force = 4.2726685e+02 on atom 13 67: Norm of force = 1.8452681e+02 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (967 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 22.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 3.1937723e+02 67: Maximum force = 9.9988691e+03 on atom 9 67: Norm of force = 4.6167015e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (377 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 3 [file glycine_vacuo.top, line 12]: 67: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 67: 67: Number of degrees of freedom in T-Coupling group System is 22.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 5 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 2.41575e+04 on atom 10 67: F-Norm = 1.18451e+04 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 1.5174414e+02 67: Maximum force = 7.4208760e+03 on atom 9 67: Norm of force = 3.5692977e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (342 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file unknown]: 67: You are using constraints on all bonds, whereas the forcefield has been 67: parametrized only with constraints involving hydrogen atoms. We suggest 67: using constraints = h-bonds instead, this will also improve performance. 67: 67: Number of degrees of freedom in T-Coupling group System is 23.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 5 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Update groups can not be used for this system because an incompatible virtual site type is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.5698444e+02 67: Maximum force = 4.5702216e+02 on atom 17 67: Norm of force = 1.8327095e+02 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 67: 67: turning all bonds into constraints... 67: 67: Cleaning up constraints and constant bonded interactions with virtual sites 67: 67: Removed 18 Angles with virtual sites, 21 left 67: 67: Removed 10 Proper Dih.s with virtual sites, 44 left 67: 67: Converted 15 Constraints with virtual sites to connections, 7 left 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (227 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file unknown]: 67: You are using constraints on all bonds, whereas the forcefield has been 67: parametrized only with constraints involving hydrogen atoms. We suggest 67: using constraints = h-bonds instead, this will also improve performance. 67: 67: 67: NOTE 4 [file unknown]: 67: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 67: 67: Number of degrees of freedom in T-Coupling group System is 23.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 6 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Update groups can not be used for this system because an incompatible virtual site type is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 1.06799e+03 on atom 28 67: F-Norm = 4.26914e+02 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.6941235e+02 67: Maximum force = 2.1838167e+02 on atom 17 67: Norm of force = 7.9235206e+01 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 67: 67: turning all bonds into constraints... 67: 67: Cleaning up constraints and constant bonded interactions with virtual sites 67: 67: Removed 18 Angles with virtual sites, 21 left 67: 67: Removed 10 Proper Dih.s with virtual sites, 44 left 67: 67: Converted 15 Constraints with virtual sites to connections, 7 left 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (336 ms) 67: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3038 ms total) 67: 67: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents converged to Fmax < 10 in 1 steps 67: Potential Energy = -9.7425687e-01 67: Maximum force = 4.0132279e+00 on atom 1 67: Norm of force = 1.6383933e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (40 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 4.01323e+00 on atom 1 67: F-Norm = 1.63839e+00 67: 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 67: Potential Energy = -9.9064195e-01 67: Maximum force = 2.5781672e+00 on atom 1 67: Norm of force = 1.0525324e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (48 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Low-Memory BFGS Minimizer: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: Using 10 BFGS correction steps. 67: 67: F-max = 4.01323e+00 on atom 1 67: F-Norm = 1.63839e+00 67: 67: 67: writing lowest energy coordinates. 67: 67: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 67: Potential Energy = -9.9064195e-01 67: Maximum force = 2.5781672e+00 on atom 1 67: Norm of force = 1.0525324e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (60 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 3.1939673e+02 67: Maximum force = 9.9704229e+03 on atom 9 67: Norm of force = 4.6227534e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (387 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 2.41672e+04 on atom 10 67: F-Norm = 1.19357e+04 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 1.5625757e+02 67: Maximum force = 7.5018237e+03 on atom 9 67: Norm of force = 3.6139019e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (410 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Low-Memory BFGS Minimizer: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: Using 10 BFGS correction steps. 67: 67: F-max = 2.41672e+04 on atom 10 67: F-Norm = 1.19357e+04 67: 67: 67: Energy minimization has stopped, but the forces have not converged to the 67: requested precision Fmax < 10 (which may not be possible for your system). It 67: stopped because the algorithm tried to make a new step whose size was too 67: small, or there was no change in the energy since last step. Either way, we 67: regard the minimization as converged to within the available machine 67: precision, given your starting configuration and EM parameters. 67: 67: Double precision normally gives you higher accuracy, but this is often not 67: needed for preparing to run molecular dynamics. 67: 67: writing lowest energy coordinates. 67: 67: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 67: but did not reach the requested Fmax < 10. 67: Potential Energy = 5.6111578e+02 67: Maximum force = 1.2685402e+04 on atom 10 67: Norm of force = 6.0643536e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (293 ms) 67: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1265 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 12 tests from 2 test suites ran. (4362 ms total) 67: [ PASSED ] 12 tests. 67/87 Test #67: Minimize1RankTests ........................ Passed 4.43 sec test 68 Start 68: Minimize2RankTests 68: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/Minimize2RankTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 12 tests from 2 test suites. 68: [----------] Global test environment set-up. 68: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -4.7990952e+01 68: Maximum force = 1.8629709e+02 on atom 13 68: Norm of force = 8.7721970e+01 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2230 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 3.02331e+02 on atom 3 68: F-Norm = 1.18024e+02 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -5.5862202e+01 68: Maximum force = 4.2727243e+02 on atom 13 68: Norm of force = 1.8452909e+02 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (3654 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 22.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 3.1937720e+02 68: Maximum force = 9.9988691e+03 on atom 9 68: Norm of force = 4.6167015e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: turning H bonds into constraints... 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (965 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: 68: NOTE 3 [file glycine_vacuo.top, line 12]: 68: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 68: 68: Number of degrees of freedom in T-Coupling group System is 22.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 2.41575e+04 on atom 10 68: F-Norm = 1.18451e+04 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 1.5174358e+02 68: Maximum force = 7.4208833e+03 on atom 9 68: Norm of force = 3.5692986e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: turning H bonds into constraints... 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (4068 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -1.5698444e+02 68: Maximum force = 4.5702219e+02 on atom 17 68: Norm of force = 1.8327095e+02 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1061 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: 68: NOTE 4 [file unknown]: 68: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 1.06799e+03 on atom 28 68: F-Norm = 4.26914e+02 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -1.6941229e+02 68: Maximum force = 2.1838167e+02 on atom 17 68: Norm of force = 7.9235200e+01 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (1809 ms) 68: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (13790 ms total) 68: 68: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents converged to Fmax < 10 in 1 steps 68: Potential Energy = -9.7425687e-01 68: Maximum force = 4.0132279e+00 on atom 3 68: Norm of force = 1.6383933e+00 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (356 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 4.01323e+00 on atom 3 68: F-Norm = 1.63839e+00 68: 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 68: Potential Energy = -9.9064195e-01 68: Maximum force = 2.5781672e+00 on atom 3 68: Norm of force = 1.0525324e+00 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (679 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: 68: There was 1 WARNING 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 3.1939664e+02 68: Maximum force = 9.9704229e+03 on atom 9 68: Norm of force = 4.6227537e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (2749 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 2.41672e+04 on atom 10 68: F-Norm = 1.19357e+04 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 1.5625764e+02 68: Maximum force = 7.5018237e+03 on atom 9 68: Norm of force = 3.6139019e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1171 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (206 ms) 68: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (5166 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 12 tests from 2 test suites ran. (19005 ms total) 68: [ PASSED ] 12 tests. 68/87 Test #68: Minimize2RankTests ........................ Passed 19.07 sec test 69 Start 69: MdrunNonIntegratorTests 69: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 46 tests from 3 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from NonbondedBenchTest 69: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 69: SIMD width: 4 69: System size: 3000 atoms 69: Cut-off radius: 1 nm 69: Number of threads: 1 69: Number of iterations: 1 69: Compute energies: no 69: Ewald excl. corr.: analytical 69: 69: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 69: total useful 69: Ewald all geom. 4xM 0.319 0.3193 3.7274 1.9720 69: [ OK ] NonbondedBenchTest.BasicEndToEndTest (43 ms) 69: [----------] 1 test from NonbondedBenchTest (59 ms total) 69: 69: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.180 0.090 199.9 69: (ns/day) (hour/ns) 69: Performance: 16.351 1.468 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 69: 69: trr version: GMX_trn_file (single precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 49 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.053 0.027 196.3 69: (ns/day) (hour/ns) 69: Performance: 54.700 0.439 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (157 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.198 0.099 199.9 69: (ns/day) (hour/ns) 69: Performance: 14.835 1.618 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 69 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.058 0.029 199.8 69: (ns/day) (hour/ns) 69: Performance: 50.490 0.475 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (150 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.178 0.089 199.9 69: (ns/day) (hour/ns) 69: Performance: 16.519 1.453 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 63 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.059 0.029 199.8 69: (ns/day) (hour/ns) 69: Performance: 49.800 0.482 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (131 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.215 0.108 199.9 69: (ns/day) (hour/ns) 69: Performance: 13.633 1.760 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 49 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.082 0.041 199.9 69: (ns/day) (hour/ns) 69: Performance: 35.910 0.668 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (168 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 398.997 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.329 0.164 199.9 69: (ns/day) (hour/ns) 69: Performance: 8.929 2.688 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 49 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.088 0.044 199.8 69: (ns/day) (hour/ns) 69: Performance: 33.225 0.722 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (859 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: NVE simulation: will use the initial temperature of 398.997 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.304 0.152 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.653 2.486 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 44 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.047 0.023 199.7 69: (ns/day) (hour/ns) 69: Performance: 62.580 0.384 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (803 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.133 0.067 199.8 69: (ns/day) (hour/ns) 69: Performance: 22.041 1.089 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 44 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.053 0.026 199.7 69: (ns/day) (hour/ns) 69: Performance: 55.839 0.430 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (534 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.368 0.184 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.972 3.010 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 61 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.057 0.029 199.7 69: (ns/day) (hour/ns) 69: Performance: 51.124 0.469 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (469 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: NVE simulation: will use the initial temperature of 456.887 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 6 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.947 0.474 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.101 7.741 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 26 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.174 0.087 199.9 69: (ns/day) (hour/ns) 69: Performance: 16.829 1.426 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (634 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: NVE simulation: will use the initial temperature of 456.887 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 6 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.342 0.671 200.0 69: (ns/day) (hour/ns) 69: Performance: 2.189 10.964 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 33 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.098 0.049 199.8 69: (ns/day) (hour/ns) 69: Performance: 29.907 0.802 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (829 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.680 0.340 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.319 5.557 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 31 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.096 0.048 199.8 69: (ns/day) (hour/ns) 69: Performance: 30.451 0.788 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (570 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.079 0.540 200.0 69: (ns/day) (hour/ns) 69: Performance: 2.722 8.817 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 36 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.089 0.044 199.8 69: (ns/day) (hour/ns) 69: Performance: 33.016 0.727 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (706 ms) 69: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (6015 ms total) 69: 69: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.331 0.165 199.9 69: (ns/day) (hour/ns) 69: Performance: 8.883 2.702 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 47 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.108 0.054 199.8 69: (ns/day) (hour/ns) 69: Performance: 27.255 0.881 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (267 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.386 0.193 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.602 3.157 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 61 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.112 0.056 199.8 69: (ns/day) (hour/ns) 69: Performance: 26.161 0.917 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (308 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.385 0.193 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.622 3.149 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 61 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.097 0.048 199.8 69: (ns/day) (hour/ns) 69: Performance: 30.362 0.790 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (297 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.291 0.145 199.9 69: (ns/day) (hour/ns) 69: Performance: 10.106 2.375 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 63 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.073 0.036 199.7 69: (ns/day) (hour/ns) 69: Performance: 40.312 0.595 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (240 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.291 0.145 199.9 69: (ns/day) (hour/ns) 69: Performance: 10.104 2.375 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 52 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.089 0.045 199.8 69: (ns/day) (hour/ns) 69: Performance: 32.887 0.730 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (232 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.295 0.148 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.946 2.413 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 29 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.072 0.036 199.7 69: (ns/day) (hour/ns) 69: Performance: 40.483 0.593 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (228 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.293 0.147 199.9 69: (ns/day) (hour/ns) 69: Performance: 10.013 2.397 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 57 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.079 0.040 199.7 69: (ns/day) (hour/ns) 69: Performance: 36.969 0.649 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (227 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.298 0.149 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.853 2.436 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 43 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.047 0.024 199.7 69: (ns/day) (hour/ns) 69: Performance: 62.360 0.385 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (215 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.225 0.113 199.9 69: (ns/day) (hour/ns) 69: Performance: 13.040 1.840 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 45 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.062 0.031 199.7 69: (ns/day) (hour/ns) 69: Performance: 47.385 0.506 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (168 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.301 0.151 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.745 2.463 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 58 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.101 0.051 199.8 69: (ns/day) (hour/ns) 69: Performance: 29.050 0.826 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (229 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.321 0.160 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.151 2.623 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 55 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.133 0.067 199.8 69: (ns/day) (hour/ns) 69: Performance: 22.034 1.089 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (284 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.638 0.319 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.600 5.217 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 54 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.133 0.067 199.9 69: (ns/day) (hour/ns) 69: Performance: 22.020 1.090 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (437 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.696 0.348 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.219 5.689 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 42 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.146 0.073 199.8 69: (ns/day) (hour/ns) 69: Performance: 20.057 1.197 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (488 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.542 0.271 200.0 69: (ns/day) (hour/ns) 69: Performance: 5.418 4.429 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 60 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.102 0.051 199.8 69: (ns/day) (hour/ns) 69: Performance: 28.747 0.835 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (394 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.542 0.271 200.0 69: (ns/day) (hour/ns) 69: Performance: 5.420 4.428 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 67 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.081 0.040 199.8 69: (ns/day) (hour/ns) 69: Performance: 36.271 0.662 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (360 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.620 0.310 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.741 5.063 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 48 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.140 0.070 199.8 69: (ns/day) (hour/ns) 69: Performance: 21.014 1.142 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (421 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.508 0.254 200.0 69: (ns/day) (hour/ns) 69: Performance: 5.778 4.154 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 46 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.112 0.056 199.8 69: (ns/day) (hour/ns) 69: Performance: 26.154 0.918 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (382 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.372 0.186 200.0 69: (ns/day) (hour/ns) 69: Performance: 7.891 3.041 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 68 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.086 0.043 199.7 69: (ns/day) (hour/ns) 69: Performance: 34.214 0.701 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (278 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 10 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.375 0.187 200.0 69: (ns/day) (hour/ns) 69: Performance: 7.839 3.062 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 41 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.080 0.040 199.7 69: (ns/day) (hour/ns) 69: Performance: 36.568 0.656 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (265 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.506 0.253 200.0 69: (ns/day) (hour/ns) 69: Performance: 5.807 4.133 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 55 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.108 0.054 199.8 69: (ns/day) (hour/ns) 69: Performance: 27.059 0.887 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (355 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.487 0.244 200.0 69: (ns/day) (hour/ns) 69: Performance: 6.026 3.983 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 51 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.156 0.078 199.9 69: (ns/day) (hour/ns) 69: Performance: 18.870 1.272 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (391 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.649 0.325 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.526 5.303 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 26 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.150 0.075 199.9 69: (ns/day) (hour/ns) 69: Performance: 19.617 1.223 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (470 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.509 0.255 199.9 69: (ns/day) (hour/ns) 69: Performance: 5.770 4.160 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 18 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.112 0.056 199.8 69: (ns/day) (hour/ns) 69: Performance: 26.158 0.917 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (417 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.497 0.249 199.9 69: (ns/day) (hour/ns) 69: Performance: 5.910 4.061 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 31 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.120 0.060 199.8 69: (ns/day) (hour/ns) 69: Performance: 24.363 0.985 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (393 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.484 0.242 199.9 69: (ns/day) (hour/ns) 69: Performance: 6.072 3.953 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 38 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.084 0.042 199.8 69: (ns/day) (hour/ns) 69: Performance: 35.129 0.683 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (368 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.351 0.176 199.9 69: (ns/day) (hour/ns) 69: Performance: 8.364 2.869 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 52 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.089 0.045 199.7 69: (ns/day) (hour/ns) 69: Performance: 32.959 0.728 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (286 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.353 0.176 199.9 69: (ns/day) (hour/ns) 69: Performance: 8.323 2.883 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 38 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.086 0.043 199.8 69: (ns/day) (hour/ns) 69: Performance: 34.139 0.703 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (278 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.418 0.209 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.032 3.413 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 26 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.079 0.040 199.7 69: (ns/day) (hour/ns) 69: Performance: 37.103 0.647 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (302 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.369 0.184 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.968 3.012 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 49 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.068 0.034 199.7 69: (ns/day) (hour/ns) 69: Performance: 43.014 0.558 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (277 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.262 0.131 199.9 69: (ns/day) (hour/ns) 69: Performance: 11.224 2.138 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 38 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.078 0.039 199.7 69: (ns/day) (hour/ns) 69: Performance: 37.371 0.642 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (207 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.261 0.131 199.9 69: (ns/day) (hour/ns) 69: Performance: 11.238 2.136 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 37 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.083 0.042 199.7 69: (ns/day) (hour/ns) 69: Performance: 35.152 0.683 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (223 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.414 0.207 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.089 3.385 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 33 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.091 0.045 199.8 69: (ns/day) (hour/ns) 69: Performance: 32.358 0.742 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (319 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.461 0.230 199.9 69: (ns/day) (hour/ns) 69: Performance: 6.374 3.765 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 38 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.083 0.042 199.8 69: (ns/day) (hour/ns) 69: Performance: 35.211 0.682 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (326 ms) 69: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (10348 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 46 tests from 3 test suites ran. (16463 ms total) 69: [ PASSED ] 46 tests. 69/87 Test #69: MdrunNonIntegratorTests ................... Passed 16.51 sec test 70 Start 70: MdrunTpiTests 70: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunTpiTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 2 tests from 1 test suite. 70: [----------] Global test environment set-up. 70: [----------] 2 tests from Simple/TpiTest 70: [ RUN ] Simple/TpiTest.ReproducesOutput/0 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 1308.00 70: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: TPI is not implemented for GPUs. 70: 70: Using 1 MPI thread 70: Using 1 OpenMP thread 70: 70: 70: NOTE: Thread affinity was not set. 70: Reading frames from gro file '216 water molecules', 648 atoms. 70: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 70: Last frame 0 time 0.000 70: Generated 331705 of the 331705 non-bonded parameter combinations 70: 70: Generated 331705 of the 331705 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Excluding 3 bonded neighbours molecule type 'methane' 70: Analysing residue names: 70: There are: 216 Water residues 70: There are: 1 Other residues 70: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] Simple/TpiTest.ReproducesOutput/0 (495 ms) 70: [ RUN ] Simple/TpiTest.ReproducesOutput/1 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 1308.00 70: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: TPI is not implemented for GPUs. 70: 70: Using 1 MPI thread 70: Using 1 OpenMP thread 70: 70: 70: NOTE: Thread affinity was not set. 70: Reading frames from gro file '216 water molecules', 648 atoms. 70: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 70: Last frame 0 time 0.000 70: Generated 331705 of the 331705 non-bonded parameter combinations 70: 70: Generated 331705 of the 331705 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Excluding 3 bonded neighbours molecule type 'methane' 70: Analysing residue names: 70: There are: 216 Water residues 70: There are: 1 Other residues 70: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] Simple/TpiTest.ReproducesOutput/1 (435 ms) 70: [----------] 2 tests from Simple/TpiTest (931 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 2 tests from 1 test suite ran. (954 ms total) 70: [ PASSED ] 2 tests. 70/87 Test #70: MdrunTpiTests ............................. Passed 0.99 sec test 71 Start 71: MdrunMpiTests 71: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMpiTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 16 tests from 2 test suites. 71: [----------] Global test environment set-up. 71: [----------] 4 tests from MimicTest 71: [ RUN ] MimicTest.OneQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 66 % of the run time was spent in domain decomposition, 71: 2 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.341 0.085 399.9 71: (ns/day) (hour/ns) 71: Performance: 1.013 23.701 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -369787777 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.OneQuantumMol (288 ms) 71: [ RUN ] MimicTest.AllQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 67 % of the run time was spent in domain decomposition, 71: 4 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.456 0.114 399.9 71: (ns/day) (hour/ns) 71: Performance: 0.758 31.665 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -134350926 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.AllQuantumMol (200 ms) 71: [ RUN ] MimicTest.TwoQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 85 % of the run time was spent in domain decomposition, 71: 1 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: NOTE: 7 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.446 0.636 384.8 71: (ns/day) (hour/ns) 71: Performance: 0.136 176.582 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -370557189 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.TwoQuantumMol (2083 ms) 71: [ RUN ] MimicTest.BondCuts 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 66.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: NVE simulation: will use the initial temperature of 300.368 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 71: 71: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 41 % of the run time was spent in domain decomposition, 71: 14 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.798 0.200 399.9 71: (ns/day) (hour/ns) 71: Performance: 0.433 55.446 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -872415297 71: 71: Generated 2211 of the 2211 non-bonded parameter combinations 71: 71: Generated 2211 of the 2211 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.BondCuts (711 ms) 71: [----------] 4 tests from MimicTest (3284 ms total) 71: 71: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There was 1 NOTE 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 9.00 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 9.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There was 1 NOTE 71: Setting the LD random seed to -1212170244 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -138044433 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -386545665 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -35651585 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was turned on during the run due to measured imbalance. 71: Average load imbalance: 28.2%. 71: The balanceable part of the MD step is 52%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 14.7%. 71: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 71: 71: NOTE: 14.7 % of the available CPU time was lost due to load imbalance 71: in the domain decomposition. 71: You can consider manually changing the decomposition (option -dd); 71: e.g. by using fewer domains along the box dimension in which there is 71: considerable inhomogeneity in the simulated system. 71: 71: NOTE: 12 % of the run time was spent in domain decomposition, 71: 1 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: NOTE: 9 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 3.769 0.952 395.9 71: (ns/day) (hour/ns) 71: Performance: 1.906 12.591 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (1454 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 8 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 4.821 1.247 386.5 71: (ns/day) (hour/ns) 71: Performance: 1.455 16.498 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1559 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was turned on during the run due to measured imbalance. 71: Average load imbalance: 51.1%. 71: The balanceable part of the MD step is 15%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 7.5%. 71: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 71: 71: NOTE: 7.5 % of the available CPU time was lost due to load imbalance 71: in the domain decomposition. 71: You can consider manually changing the decomposition (option -dd); 71: e.g. by using fewer domains along the box dimension in which there is 71: considerable inhomogeneity in the simulated system. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 12.370 3.093 400.0 71: (ns/day) (hour/ns) 71: Performance: 0.587 40.908 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (49022 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 5.218 1.305 400.0 71: (ns/day) (hour/ns) 71: Performance: 1.391 17.256 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (29270 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 10 to 100, rlist from 1 to 1 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 15.098 3.817 395.5 71: (ns/day) (hour/ns) 71: Performance: 0.475 50.491 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (5898 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 10 to 100, rlist from 1 to 1 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 4.079 1.066 382.8 71: (ns/day) (hour/ns) 71: Performance: 1.702 14.097 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (1691 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (88898 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 16 tests from 2 test suites ran. (92252 ms total) 71: [ PASSED ] 10 tests. 71: [ SKIPPED ] 6 tests, listed below: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71/87 Test #71: MdrunMpiTests ............................. Passed 92.29 sec test 72 Start 72: MdrunMultiSimTests 72: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMultiSimTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 2 tests from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from InNvt/MultiSimTerminationTest 72: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 72: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 72: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 72: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 72: [----------] 2 tests from InNvt/MultiSimTerminationTest (0 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 2 tests from 1 test suite ran. (43 ms total) 72: [ PASSED ] 2 tests. 72: 72: YOU HAVE 4 DISABLED TESTS 72: 72/87 Test #72: MdrunMultiSimTests ........................ Passed 0.11 sec test 73 Start 73: MdrunMultiSimReplexTests 73: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMultiSimReplexTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 73: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 73: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 73: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (40 ms total) 73: [ PASSED ] 1 test. 73: 73: YOU HAVE 4 DISABLED TESTS 73: 73/87 Test #73: MdrunMultiSimReplexTests .................. Passed 0.11 sec test 74 Start 74: MdrunMultiSimReplexEquivalenceTests 74: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 0 tests from 0 test suites. 74: [==========] 0 tests from 0 test suites ran. (0 ms total) 74: [ PASSED ] 0 tests. 74: 74: YOU HAVE 10 DISABLED TESTS 74: 74/87 Test #74: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.05 sec test 75 Start 75: MdrunMpi1RankPmeTests 75: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 19 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 19 tests from ReproducesEnergies/PmeTest 75: Number of degrees of freedom in T-Coupling group rest is 12.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: NVE simulation: will use the initial temperature of 1046.791 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: The optimal PME mesh load for parallel simulations is below 0.5 75: and for highly parallel simulations between 0.25 and 0.33, 75: for higher performance, increase the cut-off and the PME grid spacing. 75: 75: 75: 75: There were 2 NOTEs 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: For a correct single-point energy evaluation with nsteps = 0, use 75: continuation = yes to avoid constraining the input coordinates. 75: 75: Number of degrees of freedom in T-Coupling group rest is 13.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: NVE simulation: will use the initial temperature of 966.268 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: The optimal PME mesh load for parallel simulations is below 0.5 75: and for highly parallel simulations between 0.25 and 0.33, 75: for higher performance, increase the cut-off and the PME grid spacing. 75: 75: 75: 75: There were 3 NOTEs 75: Setting the LD random seed to 1586690038 75: 75: Generated 8 of the 10 non-bonded parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'Methanol' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 75: 75: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Calculating fourier grid dimensions for X Y Z 75: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 75: 75: Estimate for the relative computational load of the PME mesh part: 1.00 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to -541067441 75: 75: Generated 8 of the 10 non-bonded parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'Methanol' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Searching the wall atom type(s) 75: 75: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 75: 75: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Calculating fourier grid dimensions for X Y Z 75: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 75: 75: Estimate for the relative computational load of the PME mesh part: 1.00 75: 75: This run will generate roughly 0 Mb of data 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 1.329 0.665 200.0 75: (ns/day) (hour/ns) 75: Performance: 2.730 8.790 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (52708 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 1.109 0.554 200.0 75: (ns/day) (hour/ns) 75: Performance: 3.273 7.333 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (601 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 0 steps, 0.0 ps. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.058 0.029 199.5 75: (ns/day) (hour/ns) 75: Performance: 2.985 8.040 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (140269 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.931 0.465 200.0 75: (ns/day) (hour/ns) 75: Performance: 3.899 6.155 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (513 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [----------] 19 tests from ReproducesEnergies/PmeTest (194094 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 19 tests from 1 test suite ran. (194156 ms total) 75: [ PASSED ] 4 tests. 75: [ SKIPPED ] 15 tests, listed below: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 75/87 Test #75: MdrunMpi1RankPmeTests ..................... Passed 194.20 sec test 76 Start 76: MdrunMpi2RankPmeTests 76: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 19 tests from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 19 tests from ReproducesEnergies/PmeTest 76: Number of degrees of freedom in T-Coupling group rest is 12.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: NVE simulation: will use the initial temperature of 1046.791 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Number of degrees of freedom in T-Coupling group rest is 13.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: NVE simulation: will use the initial temperature of 966.268 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 3 NOTEs 76: Setting the LD random seed to -1638965 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to -883586323 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Searching the wall atom type(s) 76: 76: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 20.8%. 76: The balanceable part of the MD step is 19%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 4.1%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: 76: NOTE: 12 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 18.568 4.668 397.8 76: (ns/day) (hour/ns) 76: Performance: 0.389 61.746 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (52274 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 13.1%. 76: The balanceable part of the MD step is 21%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 2.8%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: 76: NOTE: 12 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 15.181 3.795 400.0 76: (ns/day) (hour/ns) 76: Performance: 0.478 50.202 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (4108 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 0 steps, 0.0 ps. 76: 76: NOTE: 17 % of the run time was spent in domain decomposition, 76: 2 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 8 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 1.360 0.340 399.9 76: (ns/day) (hour/ns) 76: Performance: 0.254 94.472 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (153371 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 5.004 1.310 381.8 76: (ns/day) (hour/ns) 76: Performance: 1.385 17.334 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (30760 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 6.526 1.737 375.7 76: (ns/day) (hour/ns) 76: Performance: 1.044 22.979 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (3435 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 0 steps, 0.0 ps. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.302 0.096 313.8 76: (ns/day) (hour/ns) 76: Performance: 0.898 26.738 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (103191 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was turned on during the run due to measured imbalance. 76: Average load imbalance: 20.0%. 76: The balanceable part of the MD step is 21%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 4.1%. 76: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 76: 76: 76: NOTE: 13 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 29.408 7.404 397.2 76: (ns/day) (hour/ns) 76: Performance: 0.245 97.936 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (9800 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [----------] 19 tests from ReproducesEnergies/PmeTest (356943 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 19 tests from 1 test suite ran. (357011 ms total) 76: [ PASSED ] 7 tests. 76: [ SKIPPED ] 12 tests, listed below: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 76/87 Test #76: MdrunMpi2RankPmeTests ..................... Passed 357.09 sec test 77 Start 77: MdrunCoordinationBasicTests1Rank 77: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 77: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 77: Test timeout computed to be: 1920 77: [==========] Running 1 test from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 1 test from BasicPropagators/PeriodicActionsTest 77: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.002 0.002 98.0 77: (ns/day) (hour/ns) 77: Performance: 942.563 0.025 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 96.1 77: (ns/day) (hour/ns) 77: Performance: 2225.648 0.011 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.025 0.025 99.9 77: (ns/day) (hour/ns) 77: Performance: 59.281 0.405 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 95.2 77: (ns/day) (hour/ns) 77: Performance: 2346.893 0.010 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 95.3 77: (ns/day) (hour/ns) 77: Performance: 2437.908 0.010 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 94.8 77: (ns/day) (hour/ns) 77: Performance: 2524.833 0.010 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 77: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (183 ms) 77: [----------] 1 test from BasicPropagators/PeriodicActionsTest (183 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 1 test from 1 test suite ran. (235 ms total) 77: [ PASSED ] 1 test. 77/87 Test #77: MdrunCoordinationBasicTests1Rank .......... Passed 0.32 sec test 78 Start 78: MdrunCoordinationBasicTests2Ranks 78: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 78: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 78: Test timeout computed to be: 1920 78: [==========] Running 1 test from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 1 test from BasicPropagators/PeriodicActionsTest 78: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (1) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 1.4%. 78: The balanceable part of the MD step is 53%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.7%. 78: 78: 78: NOTE: 37 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.004 0.002 195.1 78: (ns/day) (hour/ns) 78: Performance: 779.822 0.031 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (1) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 1.2%. 78: The balanceable part of the MD step is 50%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.6%. 78: 78: 78: NOTE: 26 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.002 0.001 190.8 78: (ns/day) (hour/ns) 78: Performance: 1680.238 0.014 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 4. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 4. 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 1.2%. 78: The balanceable part of the MD step is 43%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.5%. 78: 78: 78: NOTE: 29 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.002 0.001 189.6 78: (ns/day) (hour/ns) 78: Performance: 1803.717 0.013 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 2.0%. 78: The balanceable part of the MD step is 44%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.9%. 78: 78: 78: NOTE: 31 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.001 0.001 183.4 78: (ns/day) (hour/ns) 78: Performance: 1840.082 0.013 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 19.5%. 78: The balanceable part of the MD step is 52%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 10.1%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: NOTE: 10.1 % of the available CPU time was lost due to load imbalance 78: in the domain decomposition. 78: You can consider manually changing the decomposition (option -dd); 78: e.g. by using fewer domains along the box dimension in which there is 78: considerable inhomogeneity in the simulated system. 78: 78: NOTE: 15 % of the run time was spent in domain decomposition, 78: 0 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: NOTE: 45 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 3.872 1.988 194.8 78: (ns/day) (hour/ns) 78: Performance: 0.739 32.483 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 1.8%. 78: The balanceable part of the MD step is 44%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.8%. 78: 78: 78: NOTE: 31 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.001 0.001 189.8 78: (ns/day) (hour/ns) 78: Performance: 1952.335 0.012 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 78: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (8845 ms) 78: [----------] 1 test from BasicPropagators/PeriodicActionsTest (8845 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 1 test from 1 test suite ran. (8901 ms total) 78: [ PASSED ] 1 test. 78/87 Test #78: MdrunCoordinationBasicTests2Ranks ......... Passed 8.98 sec test 79 Start 79: MdrunCoordinationCouplingTests1Rank 79: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 79: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 79: Test timeout computed to be: 1920 79: [==========] Running 25 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.002 98.0 79: (ns/day) (hour/ns) 79: Performance: 968.495 0.025 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 2612.635 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.9 79: (ns/day) (hour/ns) 79: Performance: 59.463 0.404 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 96 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 87.557 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2654.284 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2766.320 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (159 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.4 79: (ns/day) (hour/ns) 79: Performance: 2096.866 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2380.446 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.9 79: (ns/day) (hour/ns) 79: Performance: 2770.051 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2632.732 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.9 79: (ns/day) (hour/ns) 79: Performance: 2698.464 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 2713.918 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (145 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 2186.934 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2513.502 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 70.484 0.341 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.4 79: (ns/day) (hour/ns) 79: Performance: 2408.363 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.6 79: (ns/day) (hour/ns) 79: Performance: 2636.112 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2449.540 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (162 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.9 79: (ns/day) (hour/ns) 79: Performance: 2158.582 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.5 79: (ns/day) (hour/ns) 79: Performance: 2547.806 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2811.773 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2682.017 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2633.858 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2649.718 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (158 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 70.253 0.342 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2453.442 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.001 91.1 79: (ns/day) (hour/ns) 79: Performance: 2741.697 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2528.979 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2702.015 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.6 79: (ns/day) (hour/ns) 79: Performance: 2733.183 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (146 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 2163.130 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2485.112 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 87.548 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2250.034 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.6 79: (ns/day) (hour/ns) 79: Performance: 2581.976 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.4 79: (ns/day) (hour/ns) 79: Performance: 2400.855 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (159 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 2194.725 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2495.178 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2755.185 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2598.310 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 70.666 0.340 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.5 79: (ns/day) (hour/ns) 79: Performance: 2530.018 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (167 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.9 79: (ns/day) (hour/ns) 79: Performance: 2015.242 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2452.466 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2822.077 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2641.764 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.6 79: (ns/day) (hour/ns) 79: Performance: 2592.842 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 87.577 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (171 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 2141.326 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2364.911 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2869.396 0.008 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 2683.185 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2744.140 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2712.723 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (146 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 70.113 0.342 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 87.438 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 90.6 79: (ns/day) (hour/ns) 79: Performance: 2656.573 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.9 79: (ns/day) (hour/ns) 79: Performance: 2576.576 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2636.112 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2607.107 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (135 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 2140.582 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 87.381 0.275 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.4 79: (ns/day) (hour/ns) 79: Performance: 2569.055 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.4 79: (ns/day) (hour/ns) 79: Performance: 2436.944 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2435.017 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2614.853 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (143 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 2234.528 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2537.312 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 87.485 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.4 79: (ns/day) (hour/ns) 79: Performance: 2441.773 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2449.540 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2454.420 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (135 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.5 79: (ns/day) (hour/ns) 79: Performance: 2221.635 0.011 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.1 79: (ns/day) (hour/ns) 79: Performance: 2581.976 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.000 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 2856.094 0.008 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 2703.200 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 87.433 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2573.347 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (147 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.7 79: (ns/day) (hour/ns) 79: Performance: 1959.476 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.9 79: (ns/day) (hour/ns) 79: Performance: 2361.285 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2773.793 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 2570.127 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.021 2.7 79: (ns/day) (hour/ns) 79: Performance: 71.047 0.338 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.9 79: (ns/day) (hour/ns) 79: Performance: 59.056 0.406 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (175 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 1984.088 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 2393.393 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2699.647 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2597.215 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.5 79: (ns/day) (hour/ns) 79: Performance: 2525.869 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 70.645 0.340 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (171 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 2001.492 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 2237.775 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2686.696 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 2480.110 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 2583.058 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 2494.167 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (147 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 85.834 0.280 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.8 79: (ns/day) (hour/ns) 79: Performance: 1893.237 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.9 79: (ns/day) (hour/ns) 79: Performance: 1978.354 0.012 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.8 79: (ns/day) (hour/ns) 79: Performance: 2059.710 0.012 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.9 79: (ns/day) (hour/ns) 79: Performance: 2077.071 0.012 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.5 79: (ns/day) (hour/ns) 79: Performance: 2013.924 0.012 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (123 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 69.440 0.346 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.7 79: (ns/day) (hour/ns) 79: Performance: 1710.801 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.9 79: (ns/day) (hour/ns) 79: Performance: 1839.532 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.4 79: (ns/day) (hour/ns) 79: Performance: 1904.945 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 1662.330 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 69.961 0.343 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (192 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.1 79: (ns/day) (hour/ns) 79: Performance: 1542.848 0.016 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.8 79: (ns/day) (hour/ns) 79: Performance: 1599.739 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.0 79: (ns/day) (hour/ns) 79: Performance: 1995.011 0.012 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.1 79: (ns/day) (hour/ns) 79: Performance: 1823.740 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.7 79: (ns/day) (hour/ns) 79: Performance: 70.416 0.341 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 58.517 0.410 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (176 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 1614.411 0.015 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 1916.203 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 2114.136 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.021 3.5 79: (ns/day) (hour/ns) 79: Performance: 70.538 0.340 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 1672.711 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 1815.143 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (176 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.9 79: (ns/day) (hour/ns) 79: Performance: 1578.425 0.015 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.5 79: (ns/day) (hour/ns) 79: Performance: 1817.821 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 69.885 0.343 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.4 79: (ns/day) (hour/ns) 79: Performance: 1714.610 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 1836.243 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.5 79: (ns/day) (hour/ns) 79: Performance: 1881.672 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (149 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 85.583 0.280 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 1654.295 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.3 79: (ns/day) (hour/ns) 79: Performance: 1857.839 0.013 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 1777.436 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.6 79: (ns/day) (hour/ns) 79: Performance: 85.960 0.279 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.5 79: (ns/day) (hour/ns) 79: Performance: 1654.739 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (158 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.8 79: (ns/day) (hour/ns) 79: Performance: 1380.061 0.017 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.4 79: (ns/day) (hour/ns) 79: Performance: 1532.486 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 69.439 0.346 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.6 79: (ns/day) (hour/ns) 79: Performance: 1436.706 0.017 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.7 79: (ns/day) (hour/ns) 79: Performance: 1537.458 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.4 79: (ns/day) (hour/ns) 79: Performance: 1587.782 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (166 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.7 79: (ns/day) (hour/ns) 79: Performance: 83.092 0.289 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.0 79: (ns/day) (hour/ns) 79: Performance: 1163.474 0.021 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 84.097 0.285 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.9 79: (ns/day) (hour/ns) 79: Performance: 1134.339 0.021 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.2 79: (ns/day) (hour/ns) 79: Performance: 1196.464 0.020 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 84.027 0.286 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (176 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.4 79: (ns/day) (hour/ns) 79: Performance: 1243.309 0.019 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.7 79: (ns/day) (hour/ns) 79: Performance: 1462.282 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.7 79: (ns/day) (hour/ns) 79: Performance: 1545.558 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 85.191 0.282 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.8 79: (ns/day) (hour/ns) 79: Performance: 1395.694 0.017 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.0 79: (ns/day) (hour/ns) 79: Performance: 1444.453 0.017 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (142 ms) 79: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (3937 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 25 tests from 1 test suite ran. (3985 ms total) 79: [ PASSED ] 25 tests. 79/87 Test #79: MdrunCoordinationCouplingTests1Rank ....... Passed 4.07 sec test 80 Start 80: MdrunCoordinationCouplingTests2Ranks 80: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 80: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 25 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.4%. 80: The balanceable part of the MD step is 55%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 37 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.004 0.002 195.4 80: (ns/day) (hour/ns) 80: Performance: 778.639 0.031 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.3%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.7 80: (ns/day) (hour/ns) 80: Performance: 1769.015 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.6%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 2121.051 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.0%. 80: The balanceable part of the MD step is 38%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.4 80: (ns/day) (hour/ns) 80: Performance: 2094.371 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.2%. 80: The balanceable part of the MD step is 38%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.3 80: (ns/day) (hour/ns) 80: Performance: 2080.227 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.0%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.1 80: (ns/day) (hour/ns) 80: Performance: 2000.518 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1590 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.7%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 24 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.0 80: (ns/day) (hour/ns) 80: Performance: 1593.120 0.015 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.5%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: NOTE: 26 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.3 80: (ns/day) (hour/ns) 80: Performance: 1796.353 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 20.3%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 10.3%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 10.3 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 16 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 55 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.777 1.389 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.058 22.691 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 42%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1860.925 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.2%. 80: The balanceable part of the MD step is 0%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.0%. 80: 80: 80: NOTE: 97 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.061 0.031 199.7 80: (ns/day) (hour/ns) 80: Performance: 47.885 0.501 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 18.2%. 80: The balanceable part of the MD step is 46%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 8.3%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 8.3 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 47 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.077 1.039 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.414 16.972 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (7612 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.2%. 80: The balanceable part of the MD step is 53%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.6%. 80: 80: 80: NOTE: 25 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.0 80: (ns/day) (hour/ns) 80: Performance: 1495.108 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 22.0%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 10.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 10.5 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 17 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 53 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.789 0.895 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.642 14.618 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.2%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.5%. 80: 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.2 80: (ns/day) (hour/ns) 80: Performance: 1921.882 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 40%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.4 80: (ns/day) (hour/ns) 80: Performance: 1787.493 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 18.8%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 7.4%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 7.4 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 17 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 43 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.817 0.909 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.616 14.849 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.2%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.0 80: (ns/day) (hour/ns) 80: Performance: 1935.468 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (5225 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 0.9%. 80: The balanceable part of the MD step is 54%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.5%. 80: 80: 80: NOTE: 24 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 192.0 80: (ns/day) (hour/ns) 80: Performance: 1545.170 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.4%. 80: The balanceable part of the MD step is 47%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.6%. 80: 80: 80: NOTE: 25 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.5 80: (ns/day) (hour/ns) 80: Performance: 1725.415 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.5%. 80: The balanceable part of the MD step is 44%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.4 80: (ns/day) (hour/ns) 80: Performance: 2001.492 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.1%. 80: The balanceable part of the MD step is 42%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.8 80: (ns/day) (hour/ns) 80: Performance: 1804.509 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.9%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.1 80: (ns/day) (hour/ns) 80: Performance: 1879.089 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.7%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.2 80: (ns/day) (hour/ns) 80: Performance: 1806.361 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1366 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 44 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.945 0.973 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.510 15.893 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.3 80: (ns/day) (hour/ns) 80: Performance: 1856.439 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 18 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 46 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.661 0.331 200.0 80: (ns/day) (hour/ns) 80: Performance: 4.442 5.403 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 44 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.808 0.940 192.3 80: (ns/day) (hour/ns) 80: Performance: 1.563 15.357 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 45 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.816 0.944 192.4 80: (ns/day) (hour/ns) 80: Performance: 1.556 15.424 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 44 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.844 0.960 192.1 80: (ns/day) (hour/ns) 80: Performance: 1.530 15.686 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (12380 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 43 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.521 0.761 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.931 12.430 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 1797.402 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.8 80: (ns/day) (hour/ns) 80: Performance: 2037.233 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.3 80: (ns/day) (hour/ns) 80: Performance: 2023.183 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 1929.104 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.7 80: (ns/day) (hour/ns) 80: Performance: 1964.162 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3143 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.5 80: (ns/day) (hour/ns) 80: Performance: 1511.061 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.004 1.036 193.4 80: (ns/day) (hour/ns) 80: Performance: 1.418 16.928 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.964 1.014 193.7 80: (ns/day) (hour/ns) 80: Performance: 1.449 16.568 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.0 80: (ns/day) (hour/ns) 80: Performance: 1981.217 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.420 1.250 193.6 80: (ns/day) (hour/ns) 80: Performance: 1.175 20.425 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 187.8 80: (ns/day) (hour/ns) 80: Performance: 2053.874 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (8379 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 26 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.7 80: (ns/day) (hour/ns) 80: Performance: 1679.780 0.014 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.9 80: (ns/day) (hour/ns) 80: Performance: 1788.790 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.0 80: (ns/day) (hour/ns) 80: Performance: 2122.513 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 1976.767 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.4 80: (ns/day) (hour/ns) 80: Performance: 2036.560 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 1904.651 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1000 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.712 1.396 194.3 80: (ns/day) (hour/ns) 80: Performance: 1.052 22.810 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.6 80: (ns/day) (hour/ns) 80: Performance: 1939.123 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 2144.307 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 2076.721 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 44 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.792 0.932 192.3 80: (ns/day) (hour/ns) 80: Performance: 1.576 15.228 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 43 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.840 0.956 192.5 80: (ns/day) (hour/ns) 80: Performance: 1.536 15.620 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (8376 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 47 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.564 1.320 194.2 80: (ns/day) (hour/ns) 80: Performance: 1.113 21.568 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.976 1.022 193.4 80: (ns/day) (hour/ns) 80: Performance: 1.437 16.699 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.972 1.022 193.0 80: (ns/day) (hour/ns) 80: Performance: 1.437 16.699 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 55 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.116 1.088 194.4 80: (ns/day) (hour/ns) 80: Performance: 1.350 17.782 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 187.8 80: (ns/day) (hour/ns) 80: Performance: 1966.356 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 2002.794 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (10759 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 26 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.2 80: (ns/day) (hour/ns) 80: Performance: 1558.657 0.015 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 26 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.3 80: (ns/day) (hour/ns) 80: Performance: 1793.477 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.4 80: (ns/day) (hour/ns) 80: Performance: 2161.233 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.1 80: (ns/day) (hour/ns) 80: Performance: 1926.088 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.0 80: (ns/day) (hour/ns) 80: Performance: 1923.983 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1973.284 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (555 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.7 80: (ns/day) (hour/ns) 80: Performance: 1664.800 0.014 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 183.7 80: (ns/day) (hour/ns) 80: Performance: 1824.820 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 2059.022 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 2052.163 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 187.7 80: (ns/day) (hour/ns) 80: Performance: 2052.505 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 1974.233 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1147 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.8 80: (ns/day) (hour/ns) 80: Performance: 1632.810 0.015 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.7 80: (ns/day) (hour/ns) 80: Performance: 1829.698 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 2022.187 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.6 80: (ns/day) (hour/ns) 80: Performance: 2013.595 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 186.8 80: (ns/day) (hour/ns) 80: Performance: 1669.764 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 26 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.416 0.744 190.3 80: (ns/day) (hour/ns) 80: Performance: 1.974 12.156 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3976 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 192.1 80: (ns/day) (hour/ns) 80: Performance: 1514.776 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 190.3 80: (ns/day) (hour/ns) 80: Performance: 1871.099 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.7 80: (ns/day) (hour/ns) 80: Performance: 2028.513 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.5 80: (ns/day) (hour/ns) 80: Performance: 2034.206 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.5 80: (ns/day) (hour/ns) 80: Performance: 2007.362 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.8 80: (ns/day) (hour/ns) 80: Performance: 2021.524 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1159 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 26 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.7 80: (ns/day) (hour/ns) 80: Performance: 1580.247 0.015 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.044 1.054 193.9 80: (ns/day) (hour/ns) 80: Performance: 1.394 17.222 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.076 1.072 193.7 80: (ns/day) (hour/ns) 80: Performance: 1.370 17.514 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 10 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.277 0.639 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.300 10.433 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.6 80: (ns/day) (hour/ns) 80: Performance: 1992.430 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.148 1.106 194.2 80: (ns/day) (hour/ns) 80: Performance: 1.328 18.071 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (9720 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.412 1.242 194.2 80: (ns/day) (hour/ns) 80: Performance: 1.183 20.294 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.972 1.020 193.3 80: (ns/day) (hour/ns) 80: Performance: 1.440 16.666 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.9 80: (ns/day) (hour/ns) 80: Performance: 1711.514 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 35 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.5 80: (ns/day) (hour/ns) 80: Performance: 1726.140 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.0 80: (ns/day) (hour/ns) 80: Performance: 1666.376 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.7 80: (ns/day) (hour/ns) 80: Performance: 1680.009 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (5431 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 9.6%. 80: The balanceable part of the MD step is 63%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 6.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 6.1 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 46 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.016 2.508 200.0 80: (ns/day) (hour/ns) 80: Performance: 0.586 40.982 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.3%. 80: The balanceable part of the MD step is 58%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.5 80: (ns/day) (hour/ns) 80: Performance: 1225.867 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.5%. 80: The balanceable part of the MD step is 49%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 187.8 80: (ns/day) (hour/ns) 80: Performance: 1325.286 0.018 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.5%. 80: The balanceable part of the MD step is 45%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 1183.364 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 39.5%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 16.2%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 16.2 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 13 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 22 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.564 1.816 196.3 80: (ns/day) (hour/ns) 80: Performance: 0.809 29.671 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 38.7%. 80: The balanceable part of the MD step is 35%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 13.7%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 13.7 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 14 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.978 0.989 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.485 16.158 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (8588 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.5%. 80: The balanceable part of the MD step is 56%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 191.5 80: (ns/day) (hour/ns) 80: Performance: 1074.023 0.022 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.8%. 80: The balanceable part of the MD step is 59%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.1%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.8 80: (ns/day) (hour/ns) 80: Performance: 1202.419 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 53%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 1249.740 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 0.9%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.5%. 80: 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.8 80: (ns/day) (hour/ns) 80: Performance: 1192.758 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.8%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.8 80: (ns/day) (hour/ns) 80: Performance: 1288.153 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.4%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 1215.227 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (507 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.6%. 80: The balanceable part of the MD step is 59%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 191.5 80: (ns/day) (hour/ns) 80: Performance: 1099.615 0.022 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 11.1%. 80: The balanceable part of the MD step is 69%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 7.7%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 7.7 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 4.400 2.232 197.1 80: (ns/day) (hour/ns) 80: Performance: 0.658 36.468 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.4%. 80: The balanceable part of the MD step is 53%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.7%. 80: 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 187.7 80: (ns/day) (hour/ns) 80: Performance: 1204.064 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.7 80: (ns/day) (hour/ns) 80: Performance: 1155.509 0.021 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.8%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.0 80: (ns/day) (hour/ns) 80: Performance: 1118.380 0.021 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.5%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.8 80: (ns/day) (hour/ns) 80: Performance: 1209.026 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (4435 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1126.354 0.021 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.7 80: (ns/day) (hour/ns) 80: Performance: 1222.461 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.6 80: (ns/day) (hour/ns) 80: Performance: 1423.263 0.017 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.1 80: (ns/day) (hour/ns) 80: Performance: 1498.928 0.016 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 186.1 80: (ns/day) (hour/ns) 80: Performance: 1369.934 0.018 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 43 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.967 1.507 196.8 80: (ns/day) (hour/ns) 80: Performance: 0.974 24.632 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (2968 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.069 0.035 199.6 80: (ns/day) (hour/ns) 80: Performance: 42.434 0.566 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 187.5 80: (ns/day) (hour/ns) 80: Performance: 1206.068 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 184.7 80: (ns/day) (hour/ns) 80: Performance: 1283.056 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1286.136 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.566 0.283 200.0 80: (ns/day) (hour/ns) 80: Performance: 5.184 4.629 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 187.5 80: (ns/day) (hour/ns) 80: Performance: 1280.522 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (3795 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 190.4 80: (ns/day) (hour/ns) 80: Performance: 1098.537 0.022 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.614 0.307 199.9 80: (ns/day) (hour/ns) 80: Performance: 4.785 5.016 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 1390.810 0.017 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1298.060 0.018 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 7 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.0 80: (ns/day) (hour/ns) 80: Performance: 1288.423 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 1263.841 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (1968 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 65 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.123 0.062 199.7 80: (ns/day) (hour/ns) 80: Performance: 23.872 1.005 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.405 1.703 200.0 80: (ns/day) (hour/ns) 80: Performance: 0.863 27.822 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.6 80: (ns/day) (hour/ns) 80: Performance: 1150.008 0.021 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.740 0.370 199.9 80: (ns/day) (hour/ns) 80: Performance: 3.968 6.048 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 56 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 6.180 3.148 196.3 80: (ns/day) (hour/ns) 80: Performance: 0.467 51.435 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.286 0.643 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.284 10.508 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (10479 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 191.0 80: (ns/day) (hour/ns) 80: Performance: 856.828 0.028 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 190.9 80: (ns/day) (hour/ns) 80: Performance: 938.614 0.026 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 190.3 80: (ns/day) (hour/ns) 80: Performance: 914.917 0.026 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 190.8 80: (ns/day) (hour/ns) 80: Performance: 937.044 0.026 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 190.7 80: (ns/day) (hour/ns) 80: Performance: 937.971 0.026 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 190.9 80: (ns/day) (hour/ns) 80: Performance: 927.172 0.026 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (1892 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 1011.509 0.024 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 188.7 80: (ns/day) (hour/ns) 80: Performance: 1048.612 0.023 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 191.0 80: (ns/day) (hour/ns) 80: Performance: 876.890 0.027 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.922 0.961 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.528 15.702 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.0 80: (ns/day) (hour/ns) 80: Performance: 1115.847 0.022 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 4.496 2.284 196.9 80: (ns/day) (hour/ns) 80: Performance: 0.643 37.318 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (6692 ms) 80: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (123154 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 25 tests from 1 test suite ran. (123190 ms total) 80: [ PASSED ] 25 tests. 80/87 Test #80: MdrunCoordinationCouplingTests2Ranks ...... Passed 123.25 sec test 81 Start 81: MdrunCoordinationConstraintsTests1Rank 81: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 81: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 13 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 1897.319 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2043.993 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.4 81: (ns/day) (hour/ns) 81: Performance: 2642.897 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2575.499 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2471.157 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.009 0.009 99.5 81: (ns/day) (hour/ns) 81: Performance: 167.571 0.143 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2370 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 1955.744 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.9 81: (ns/day) (hour/ns) 81: Performance: 2105.466 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 90.5 81: (ns/day) (hour/ns) 81: Performance: 2410.248 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.4 81: (ns/day) (hour/ns) 81: Performance: 2204.937 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.8 81: (ns/day) (hour/ns) 81: Performance: 2424.476 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2450.515 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (2639 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 1879.376 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.5 81: (ns/day) (hour/ns) 81: Performance: 2061.778 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.697 0.339 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.576 0.340 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 2224.041 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.4 81: (ns/day) (hour/ns) 81: Performance: 2404.603 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (3808 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 1935.468 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.1 81: (ns/day) (hour/ns) 81: Performance: 2325.630 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2614.853 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2309.934 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2405.542 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.4 81: (ns/day) (hour/ns) 81: Performance: 2415.919 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (3337 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.8 81: (ns/day) (hour/ns) 81: Performance: 1917.993 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2039.932 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.7 81: (ns/day) (hour/ns) 81: Performance: 87.614 0.274 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.8 81: (ns/day) (hour/ns) 81: Performance: 2450.515 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.0 81: (ns/day) (hour/ns) 81: Performance: 2191.602 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2426.386 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2926 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 1937.294 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2233.718 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2282.547 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.3 81: (ns/day) (hour/ns) 81: Performance: 2359.477 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.7 81: (ns/day) (hour/ns) 81: Performance: 105.929 0.227 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.8 81: (ns/day) (hour/ns) 81: Performance: 2322.124 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3115 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.4 81: (ns/day) (hour/ns) 81: Performance: 1897.319 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 2124.343 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2373.110 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 2317.755 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.1 81: (ns/day) (hour/ns) 81: Performance: 2271.605 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 2259.110 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2058 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.2 81: (ns/day) (hour/ns) 81: Performance: 1876.513 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 2088.337 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.009 0.009 99.6 81: (ns/day) (hour/ns) 81: Performance: 166.287 0.144 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 2220.034 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 92.3 81: (ns/day) (hour/ns) 81: Performance: 2165.411 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2230.483 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (2272 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.8 81: (ns/day) (hour/ns) 81: Performance: 1853.925 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 2038.582 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 2345.106 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 2261.598 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 2119.227 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 2200.998 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3097 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.6 81: (ns/day) (hour/ns) 81: Performance: 1488.426 0.016 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 69.503 0.345 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.1 81: (ns/day) (hour/ns) 81: Performance: 1793.477 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.2 81: (ns/day) (hour/ns) 81: Performance: 1655.629 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.1 81: (ns/day) (hour/ns) 81: Performance: 1730.990 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.6 81: (ns/day) (hour/ns) 81: Performance: 113.513 0.211 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (3560 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.4 81: (ns/day) (hour/ns) 81: Performance: 1356.361 0.018 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.4 81: (ns/day) (hour/ns) 81: Performance: 1460.549 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.2 81: (ns/day) (hour/ns) 81: Performance: 1694.333 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1518.510 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1538.994 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.1 81: (ns/day) (hour/ns) 81: Performance: 1585.738 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (3438 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1268.917 0.019 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.6 81: (ns/day) (hour/ns) 81: Performance: 112.076 0.214 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 1794.522 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.3 81: (ns/day) (hour/ns) 81: Performance: 1621.636 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 1688.296 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.6 81: (ns/day) (hour/ns) 81: Performance: 1622.063 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2115 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.7 81: (ns/day) (hour/ns) 81: Performance: 1390.339 0.017 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.010 0.010 99.5 81: (ns/day) (hour/ns) 81: Performance: 148.555 0.162 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 1659.643 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1534.777 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1612.721 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 1609.351 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3036 ms) 81: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (37776 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 13 tests from 1 test suite ran. (37808 ms total) 81: [ PASSED ] 13 tests. 81/87 Test #81: MdrunCoordinationConstraintsTests1Rank .... Passed 37.88 sec test 82 Start 82: MdrunCoordinationConstraintsTests2Ranks 82: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 82: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 13 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.5%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.9 82: (ns/day) (hour/ns) 82: Performance: 1466.284 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.0%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 26 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.1 82: (ns/day) (hour/ns) 82: Performance: 1761.428 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 26 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.7 82: (ns/day) (hour/ns) 82: Performance: 2095.084 0.011 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.3%. 82: The balanceable part of the MD step is 36%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.5 82: (ns/day) (hour/ns) 82: Performance: 1818.894 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 31.9%. 82: The balanceable part of the MD step is 24%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 7.6%. 82: 82: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 82: in the domain decomposition. 82: You can consider manually changing the decomposition (option -dd); 82: e.g. by using fewer domains along the box dimension in which there is 82: considerable inhomogeneity in the simulated system. 82: 82: NOTE: 47 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.138 0.069 199.9 82: (ns/day) (hour/ns) 82: Performance: 21.272 1.128 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.6%. 82: The balanceable part of the MD step is 33%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 20 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 13 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.613 1.307 200.0 82: (ns/day) (hour/ns) 82: Performance: 1.124 21.349 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (8656 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.5%. 82: The balanceable part of the MD step is 0%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.0%. 82: 82: 82: NOTE: 65 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.248 0.124 199.9 82: (ns/day) (hour/ns) 82: Performance: 11.862 2.023 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.8 82: (ns/day) (hour/ns) 82: Performance: 1720.356 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 27 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 1989.856 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 43%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 1810.874 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.1 82: (ns/day) (hour/ns) 82: Performance: 1713.418 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.6%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.6 82: (ns/day) (hour/ns) 82: Performance: 1723.966 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (5905 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.5%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.9 82: (ns/day) (hour/ns) 82: Performance: 1367.198 0.018 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.1%. 82: The balanceable part of the MD step is 49%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.8 82: (ns/day) (hour/ns) 82: Performance: 1699.709 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.0%. 82: The balanceable part of the MD step is 43%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 27 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.3 82: (ns/day) (hour/ns) 82: Performance: 1923.983 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.8%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 1745.705 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.6%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 1771.304 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.3%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.1%. 82: 82: 82: NOTE: 17 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 3.319 1.685 196.9 82: (ns/day) (hour/ns) 82: Performance: 0.871 27.541 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (7216 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 4.008 2.038 196.7 82: (ns/day) (hour/ns) 82: Performance: 0.721 33.297 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 6 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.6 82: (ns/day) (hour/ns) 82: Performance: 1830.786 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 26 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 3.124 1.596 195.7 82: (ns/day) (hour/ns) 82: Performance: 0.920 26.078 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 183.9 82: (ns/day) (hour/ns) 82: Performance: 1817.821 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 183.6 82: (ns/day) (hour/ns) 82: Performance: 1811.140 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 3.224 1.650 195.4 82: (ns/day) (hour/ns) 82: Performance: 0.890 26.960 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (14223 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.8 82: (ns/day) (hour/ns) 82: Performance: 1418.021 0.017 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 14 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.093 1.047 200.0 82: (ns/day) (hour/ns) 82: Performance: 1.403 17.104 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 5 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.6 82: (ns/day) (hour/ns) 82: Performance: 1933.949 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.3 82: (ns/day) (hour/ns) 82: Performance: 1786.197 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 3.648 1.856 196.6 82: (ns/day) (hour/ns) 82: Performance: 0.791 30.324 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 3.648 1.860 196.1 82: (ns/day) (hour/ns) 82: Performance: 0.790 30.392 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (13535 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.8 82: (ns/day) (hour/ns) 82: Performance: 1409.263 0.017 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.5 82: (ns/day) (hour/ns) 82: Performance: 1662.778 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 5 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1957.297 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 181.2 82: (ns/day) (hour/ns) 82: Performance: 1764.455 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 1886.281 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 185.5 82: (ns/day) (hour/ns) 82: Performance: 1785.421 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4171 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 26 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 4.456 2.276 195.8 82: (ns/day) (hour/ns) 82: Performance: 0.645 37.189 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 4.084 2.076 196.7 82: (ns/day) (hour/ns) 82: Performance: 0.708 33.921 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 190.3 82: (ns/day) (hour/ns) 82: Performance: 1894.693 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 190.5 82: (ns/day) (hour/ns) 82: Performance: 1891.493 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.3 82: (ns/day) (hour/ns) 82: Performance: 1773.598 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.0 82: (ns/day) (hour/ns) 82: Performance: 1736.601 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (11003 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 14 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 21 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.002 1.001 200.0 82: (ns/day) (hour/ns) 82: Performance: 1.468 16.354 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.7 82: (ns/day) (hour/ns) 82: Performance: 1562.611 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.3 82: (ns/day) (hour/ns) 82: Performance: 1823.200 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 4.676 2.380 196.5 82: (ns/day) (hour/ns) 82: Performance: 0.617 38.890 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 4.829 2.455 196.7 82: (ns/day) (hour/ns) 82: Performance: 0.598 40.107 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.5 82: (ns/day) (hour/ns) 82: Performance: 1619.930 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (14492 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.5 82: (ns/day) (hour/ns) 82: Performance: 1331.301 0.018 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 4.756 2.420 196.6 82: (ns/day) (hour/ns) 82: Performance: 0.607 39.538 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.7 82: (ns/day) (hour/ns) 82: Performance: 1712.941 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.2 82: (ns/day) (hour/ns) 82: Performance: 1604.948 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.092 0.046 199.8 82: (ns/day) (hour/ns) 82: Performance: 31.874 0.753 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.5 82: (ns/day) (hour/ns) 82: Performance: 1645.238 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (9127 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.6%. 82: The balanceable part of the MD step is 59%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 5 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 191.4 82: (ns/day) (hour/ns) 82: Performance: 1059.796 0.023 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.0%. 82: The balanceable part of the MD step is 56%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.535 0.267 200.0 82: (ns/day) (hour/ns) 82: Performance: 5.494 4.368 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.0%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.6 82: (ns/day) (hour/ns) 82: Performance: 1308.676 0.018 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.7%. 82: The balanceable part of the MD step is 46%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.9 82: (ns/day) (hour/ns) 82: Performance: 1193.451 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 47%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.1 82: (ns/day) (hour/ns) 82: Performance: 1264.879 0.019 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.2%. 82: The balanceable part of the MD step is 48%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.7 82: (ns/day) (hour/ns) 82: Performance: 1296.421 0.019 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (4749 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 57%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.275 0.138 199.9 82: (ns/day) (hour/ns) 82: Performance: 10.674 2.248 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB got disabled because it was unsuitable to use. 82: Average load imbalance: 13.4%. 82: The balanceable part of the MD step is 23%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 3.1%. 82: 82: 82: NOTE: 18 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.446 1.223 200.0 82: (ns/day) (hour/ns) 82: Performance: 1.201 19.987 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 53%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 6 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.4 82: (ns/day) (hour/ns) 82: Performance: 1199.960 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 58%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 43 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 5.688 2.882 197.4 82: (ns/day) (hour/ns) 82: Performance: 0.510 47.094 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.1%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 189.9 82: (ns/day) (hour/ns) 82: Performance: 1086.141 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.0%. 82: The balanceable part of the MD step is 49%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 5 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 190.4 82: (ns/day) (hour/ns) 82: Performance: 1094.147 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (10126 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 189.6 82: (ns/day) (hour/ns) 82: Performance: 994.687 0.024 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.276 0.138 199.8 82: (ns/day) (hour/ns) 82: Performance: 10.631 2.258 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.1 82: (ns/day) (hour/ns) 82: Performance: 1213.432 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.6 82: (ns/day) (hour/ns) 82: Performance: 1192.527 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.9 82: (ns/day) (hour/ns) 82: Performance: 1174.117 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 27 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 7.004 3.546 197.5 82: (ns/day) (hour/ns) 82: Performance: 0.414 57.938 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (11144 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 985.380 0.024 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.6 82: (ns/day) (hour/ns) 82: Performance: 1073.274 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.0 82: (ns/day) (hour/ns) 82: Performance: 1174.341 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.2 82: (ns/day) (hour/ns) 82: Performance: 1133.295 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.8 82: (ns/day) (hour/ns) 82: Performance: 1118.583 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.3 82: (ns/day) (hour/ns) 82: Performance: 1156.702 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (5530 ms) 82: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (119886 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 13 tests from 1 test suite ran. (119898 ms total) 82: [ PASSED ] 13 tests. 82/87 Test #82: MdrunCoordinationConstraintsTests2Ranks ... Passed 119.97 sec test 83 Start 83: MdrunFEPTests 83: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunFEPTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -1048577 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.188 1.094 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.658 14.473 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (39584 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -117721477 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.501 1.250 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.451 16.541 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (1650 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 4 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to 2011162617 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.908 0.954 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.902 12.620 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (1337 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 3 [file topol.top, line 155]: 83: System has non-zero total charge: 1.000000 83: Total charge should normally be an integer. See 83: https://manual.gromacs.org/current/user-guide/floating-point.html 83: for discussion on how close it should be to an integer. 83: 83: 83: 83: 83: WARNING 2 [file topol.top, line 155]: 83: You are using Ewald electrostatics in a system with net charge. This can 83: lead to severe artifacts, such as ions moving into regions with low 83: dielectric, due to the uniform background charge. We suggest to 83: neutralize your system with counter ions, possibly in combination with a 83: physiological salt concentration. 83: 83: Setting the LD random seed to -822149427 83: 83: Generated 171 of the 171 non-bonded parameter combinations 83: 83: Generated 171 of the 171 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'NA' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: 83: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 83: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 83: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 83: Charge 83: J. Chem. Theory Comput. 10 (2014) pp. 381-393 83: -------- -------- --- Thank You --- -------- -------- 83: 83: Number of degrees of freedom in T-Coupling group System is 358.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 5 NOTEs 83: 83: There were 2 WARNINGs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: There are: 1 Ion residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 83: 83: Estimate for the relative computational load of the PME mesh part: 0.96 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.907 0.954 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.903 12.613 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (49225 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 3 [file topol.top, line 165]: 83: System has non-zero total charge: 1.000000 83: Total charge should normally be an integer. See 83: https://manual.gromacs.org/current/user-guide/floating-point.html 83: for discussion on how close it should be to an integer. 83: 83: 83: 83: 83: WARNING 2 [file topol.top, line 165]: 83: You are using Ewald electrostatics in a system with net charge. This can 83: lead to severe artifacts, such as ions moving into regions with low 83: dielectric, due to the uniform background charge. We suggest to 83: neutralize your system with counter ions, possibly in combination with a 83: physiological salt concentration. 83: 83: Setting the LD random seed to 1040104948 83: 83: Generated 190 of the 190 non-bonded parameter combinations 83: 83: Generated 190 of the 190 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'NA' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'CL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'CL' 83: 83: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 83: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 83: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 83: Charge 83: J. Chem. Theory Comput. 10 (2014) pp. 381-393 83: -------- -------- --- Thank You --- -------- -------- 83: 83: Number of degrees of freedom in T-Coupling group System is 361.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 5 NOTEs 83: 83: There were 2 WARNINGs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: There are: 2 Ion residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 83: 83: Estimate for the relative computational load of the PME mesh part: 0.96 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.484 0.242 199.9 83: (ns/day) (hour/ns) 83: Performance: 7.490 3.204 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (310 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 83: and vdw_modifier=Force-switch 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 4 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 100 steps, 0.1 ps. 83: Setting the LD random seed to 2147466719 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 8.430 4.215 200.0 83: (ns/day) (hour/ns) 83: Performance: 2.070 11.592 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (4495 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: WARNING 2 [file topol.top, line 72]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 3 [file topol.top, line 73]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 4 [file topol.top, line 98]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 5 [file topol.top, line 99]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 6 [file topol.top, line 100]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 7 [file topol.top, line 101]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 8 [file topol.top, line 111]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 9 [file topol.top, line 112]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 10 [file topol.top, line 113]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 11 [file topol.top, line 114]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 2 NOTEs 83: 83: There were 11 WARNINGs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to 1842020135 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.95 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.786 1.393 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.303 18.426 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (1682 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: WARNING 2 [file topol.top, line 72]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 3 [file topol.top, line 73]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 4 [file topol.top, line 98]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 5 [file topol.top, line 99]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 6 [file topol.top, line 100]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 7 [file topol.top, line 101]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 8 [file topol.top, line 111]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 9 [file topol.top, line 112]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 10 [file topol.top, line 113]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 11 [file topol.top, line 114]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: Removing center of mass motion in the presence of position restraints 83: might cause artifacts. When you are using position restraints to 83: equilibrate a macro-molecule, the artifacts are usually negligible. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There were 11 WARNINGs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -239208473 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.94 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.644 1.322 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.372 17.488 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (1640 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -536904706 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.89 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.138 0.569 200.0 83: (ns/day) (hour/ns) 83: Performance: 3.189 7.526 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (833 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: There was 1 NOTE 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.164 0.582 200.0 83: (ns/day) (hour/ns) 83: Performance: 3.117 7.699 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -946080522 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.90 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (882 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -1073775953 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.95 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.018 0.509 200.0 83: (ns/day) (hour/ns) 83: Performance: 3.563 6.736 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (628 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to 2104450303 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.90 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.804 0.402 200.0 83: (ns/day) (hour/ns) 83: Performance: 4.510 5.321 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (510 ms) 83: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (102782 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 1 test suite ran. (102822 ms total) 83: [ PASSED ] 12 tests. 83/87 Test #83: MdrunFEPTests ............................. Passed 102.88 sec test 84 Start 84: MdrunPullTests 84: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunPullTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 4 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 4 tests from PullTest/PullIntegrationTest 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.600 nm 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.306 0.153 199.9 84: (ns/day) (hour/ns) 84: Performance: 11.835 2.028 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (533 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.301 nm 0.400 nm 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.413 0.206 199.9 84: (ns/day) (hour/ns) 84: Performance: 8.792 2.730 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (729 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Pull group 3 'r_3' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1292.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.357 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.500 nm 84: 1 3 2 84: 3 3 8 0.331 nm 0.400 nm 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.388 0.194 199.9 84: (ns/day) (hour/ns) 84: Performance: 9.360 2.564 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (686 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.000 nm 84: 1 3 2 84: 2 3 5 0.050 nm 0.000 nm 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.391 0.195 199.9 84: (ns/day) (hour/ns) 84: Performance: 9.282 2.586 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (691 ms) 84: [----------] 4 tests from PullTest/PullIntegrationTest (2640 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 4 tests from 1 test suite ran. (2655 ms total) 84: [ PASSED ] 4 tests. 84/87 Test #84: MdrunPullTests ............................ Passed 2.71 sec test 85 Start 85: MdrunRotationTests 85: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunRotationTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 12 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 12 tests from RotationWorks/RotationTest 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 85: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: trr version: GMX_trn_file (single precision) 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -16810409 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.056 0.028 199.6 85: (ns/day) (hour/ns) 85: Performance: 159.891 0.150 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (94 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 85: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 1702354747 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.511 0.256 199.9 85: (ns/day) (hour/ns) 85: Performance: 17.572 1.366 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (301 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 85: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -310460429 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.391 0.196 199.9 85: (ns/day) (hour/ns) 85: Performance: 22.959 1.045 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (232 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 85: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 2088422719 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.400 0.200 199.9 85: (ns/day) (hour/ns) 85: Performance: 22.452 1.069 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (228 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 85: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -16875521 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.401 0.201 199.9 85: (ns/day) (hour/ns) 85: Performance: 22.382 1.072 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (221 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 85: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -172495025 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 11 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.391 0.195 199.9 85: (ns/day) (hour/ns) 85: Performance: 22.988 1.044 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (221 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 85: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -83919127 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 19 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.397 0.199 199.9 85: (ns/day) (hour/ns) 85: Performance: 22.623 1.061 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (225 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 85: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -4596401 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 11 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.401 0.201 199.9 85: (ns/day) (hour/ns) 85: Performance: 22.393 1.072 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (221 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 85: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -268 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.288 0.144 199.9 85: (ns/day) (hour/ns) 85: Performance: 31.163 0.770 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (170 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 85: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -33945890 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.301 0.151 199.9 85: (ns/day) (hour/ns) 85: Performance: 29.794 0.806 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (169 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 85: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -148897793 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 10 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.310 0.155 199.9 85: (ns/day) (hour/ns) 85: Performance: 28.977 0.828 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (170 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 85: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1377997877 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.289 0.145 199.9 85: (ns/day) (hour/ns) 85: Performance: 31.048 0.773 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (162 ms) 85: [----------] 12 tests from RotationWorks/RotationTest (2419 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 12 tests from 1 test suite ran. (2459 ms total) 85: [ PASSED ] 12 tests. 85/87 Test #85: MdrunRotationTests ........................ Passed 2.52 sec test 86 Start 86: MdrunSimulatorComparison 86: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunSimulatorComparison.xml" 86: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 0 tests from 0 test suites. 86: [==========] 0 tests from 0 test suites ran. (0 ms total) 86: [ PASSED ] 0 tests. 86: 86: YOU HAVE 82 DISABLED TESTS 86: 86/87 Test #86: MdrunSimulatorComparison .................. Passed 0.06 sec test 87 Start 87: MdrunVirtualSiteTests 87: Test command: /build/reproducible-path/gromacs-2024.4/build/basic/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic/Testing/Temporary/MdrunVirtualSiteTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 37 tests from 2 test suites. 87: [----------] Global test environment set-up. 87: [----------] 1 test from VirtualSiteVelocityTest 87: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 87: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 87: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 87: 87: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.4%. 87: The balanceable part of the MD step is 41%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.0%. 87: 87: 87: NOTE: 39 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.003 0.002 194.4 87: (ns/day) (hour/ns) 87: Performance: 457.047 0.053 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: trr version: GMX_trn_file (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (238 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.1%. 87: The balanceable part of the MD step is 38%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.4%. 87: 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.1 87: (ns/day) (hour/ns) 87: Performance: 883.514 0.027 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (240 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 21.5%. 87: The balanceable part of the MD step is 31%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 6.7%. 87: 87: NOTE: 6.7 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 87: You can also consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: NOTE: 26 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 10 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.148 1.108 193.9 87: (ns/day) (hour/ns) 87: Performance: 0.702 34.197 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (2631 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 1086.620 0.022 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (87 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 187.9 87: (ns/day) (hour/ns) 87: Performance: 1063.587 0.023 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (167 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 187.8 87: (ns/day) (hour/ns) 87: Performance: 1054.645 0.023 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (251 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 31 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 1024.016 0.023 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (255 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 80 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.046 0.023 199.3 87: (ns/day) (hour/ns) 87: Performance: 33.997 0.706 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (220 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.1 87: (ns/day) (hour/ns) 87: Performance: 962.660 0.025 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (171 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 37%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 185.1 87: (ns/day) (hour/ns) 87: Performance: 923.804 0.026 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (103 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 1.2%. 87: The balanceable part of the MD step is 42%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.5%. 87: 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 186.1 87: (ns/day) (hour/ns) 87: Performance: 960.958 0.025 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (51 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.4 87: (ns/day) (hour/ns) 87: Performance: 1059.958 0.023 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (147 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 11 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 26 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.660 1.378 193.0 87: (ns/day) (hour/ns) 87: Performance: 0.564 42.530 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (3032 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 976.348 0.025 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (231 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 949.903 0.025 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (127 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 988.630 0.024 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (355 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.0 87: (ns/day) (hour/ns) 87: Performance: 1053.623 0.023 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (192 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.8 87: (ns/day) (hour/ns) 87: Performance: 1057.895 0.023 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (211 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.8 87: (ns/day) (hour/ns) 87: Performance: 1042.176 0.023 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (159 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 189.0 87: (ns/day) (hour/ns) 87: Performance: 999.384 0.024 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (195 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.001 0.001 188.3 87: (ns/day) (hour/ns) 87: Performance: 1008.033 0.024 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (590 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 87: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (9669 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 37 tests from 2 test suites ran. (9692 ms total) 87: [ PASSED ] 37 tests. 87/87 Test #87: MdrunVirtualSiteTests ..................... Passed 9.73 sec 100% tests passed, 0 tests failed out of 87 Label Time Summary: GTest = 4957.93 sec*proc (85 tests) IntegrationTest = 4346.02 sec*proc (28 tests) MpiTest = 3895.37 sec*proc (21 tests) QuickGpuTest = 530.01 sec*proc (20 tests) SlowGpuTest = 4362.26 sec*proc (14 tests) SlowTest = 590.06 sec*proc (13 tests) UnitTest = 21.85 sec*proc (44 tests) Total Test time (real) = 1860.10 sec /usr/bin/make -j12 -C build/basic-dp tests make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E 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src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd 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cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 66%] Built target gtest /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/basic-dp 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -MD -MT src/external/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o -MF CMakeFiles/gmock.dir/src/gmock-all.cc.o.d -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 66%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/testutils /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/mpitest.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/energycomparison.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/testsystems.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -MF CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o.d -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/calc_verletbuf.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/terminationhelper.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -MF CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o.d -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constr.cpp.o -MF CMakeFiles/mdlib-test.dir/constr.cpp.o.d -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/bonded.cpp.o -MF CMakeFiles/listed_forces-test.dir/bonded.cpp.o.d -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/bonded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.9.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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--verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target testutils-test /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/fft.cpp.o -MF CMakeFiles/fft-test.dir/fft.cpp.o.d -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, LJCombinationRule)': /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:186:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 186 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-test.dir/link.d "CMakeFiles/domdec-test.dir/hashedmap.cpp.o" "CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o" "CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 68%] Built target domdec-test /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energyoutput.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/domdec-mpi-test.dir/link.d "CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o" "CMakeFiles/domdec-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/domdec-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 69%] Built target domdec-mpi-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernelsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fft/tests/CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 69%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/colvars_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/colvars_applied_forces-test.dir/link.d "CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o" "CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/colvars_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 69%] Built target colvars_applied_forces-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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--verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target fft-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/enerdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/boxmatrix.cpp.o -MF CMakeFiles/math-test.dir/boxmatrix.cpp.o.d -o CMakeFiles/math-test.dir/boxmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/boxmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/expanded.cpp.o -MF CMakeFiles/mdlib-test.dir/expanded.cpp.o.d -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nbnxm-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/observablesreducer.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target nbnxm-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/booltype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f 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src/gromacs/options/tests/CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -MF CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o.d -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/layouts.cpp.o -MF CMakeFiles/mdspan-test.dir/layouts.cpp.o.d -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/layouts.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem 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CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/mdspan.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target listed_forces-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/com.cpp.o -MF CMakeFiles/pbcutil-test.dir/com.cpp.o.d -o CMakeFiles/pbcutil-test.dir/com.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/com.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfit.cpp.o -MF CMakeFiles/math-test.dir/densityfit.cpp.o.d -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/densityfit.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/device_management.cpp.o -MF CMakeFiles/hardware-test.dir/device_management.cpp.o.d -o CMakeFiles/hardware-test.dir/device_management.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/device_management.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrog.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrog.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true 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CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target hardware-test /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -MF CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true 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src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/dofit.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/cstringutil.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target gpu_utils-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/defaultinitializationallocator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdspan-test.dir/link.d "CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o" "CMakeFiles/mdspan-test.dir/extents.cpp.o" "CMakeFiles/mdspan-test.dir/extensions.cpp.o" "CMakeFiles/mdspan-test.dir/layouts.cpp.o" "CMakeFiles/mdspan-test.dir/mdspan.cpp.o" "CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target mdspan-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make 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src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 70%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/enumerationhelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 72%] Built target awh-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -MF CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o.d -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/timing-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target taskassignment-test /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target timing-test /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/pull.cpp.o -MF CMakeFiles/pull-test.dir/pull.cpp.o.d -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/tests/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/seed.cpp.o -MF CMakeFiles/random-test.dir/seed.cpp.o.d -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/seed.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include 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-DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -MF CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o.d -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target pbcutil-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/gausstransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/option.cpp.o -MF CMakeFiles/options-test.dir/option.cpp.o.d -o CMakeFiles/options-test.dir/option.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/option.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -MF CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o.d -o CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/optionsassigner.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target pull-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/entropy.cpp.o -MF CMakeFiles/gmxana-test.dir/entropy.cpp.o.d -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/entropy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/pointers.cpp.o -MF CMakeFiles/compat-test.dir/pointers.cpp.o.d -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests/pointers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target table-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_traj.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/shake.cpp.o -MF CMakeFiles/mdlib-test.dir/shake.cpp.o.d -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/shake.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformintdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar_util.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target mdtypes-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/invertmatrix.cpp.o -MF CMakeFiles/math-test.dir/invertmatrix.cpp.o.d -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/invertmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target gmxana-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -MF CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o.d -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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-DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd.cpp.o -MF CMakeFiles/simd-test.dir/simd.cpp.o.d -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 73%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/repeatingsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/grompp_directives.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/timeunitmanager.cpp.o -MF CMakeFiles/options-test.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" 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"CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 77%] Built target mdlib-test /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/energyterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/register.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 78%] Built target topology-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/optimization.cpp.o -MF CMakeFiles/math-test.dir/optimization.cpp.o.d -o CMakeFiles/math-test.dir/optimization.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/optimization.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringutil.cpp.o -MF CMakeFiles/utility-test.dir/stringutil.cpp.o.d -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/stringutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -MF CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o.d -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 80%] Built target correlations-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/make_ndx.cpp.o -MF CMakeFiles/tool-test.dir/make_ndx.cpp.o.d -o CMakeFiles/tool-test.dir/make_ndx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/make_ndx.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 80%] Built target energyanalysis-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -MF CMakeFiles/coordinateio-test.dir/testmodule.cpp.o.d -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/testmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/confio.cpp.o -MF CMakeFiles/fileio-test.dir/confio.cpp.o.d -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/confio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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"CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 80%] Built target analysisdata-test-shared /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 81%] Built target options-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/trjconv.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_math.cpp.o -MF CMakeFiles/simd-test.dir/simd_math.cpp.o.d -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/solvate.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 81%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -MF CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/outputfiles.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filemd5.cpp.o -MF CMakeFiles/fileio-test.dir/filemd5.cpp.o.d -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filemd5.cpp /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp:169:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 169 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/topdirs.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/filetypes.cpp.o -MF CMakeFiles/fileio-test.dir/filetypes.cpp.o.d 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/convert-tpr.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxpreprocess-test.dir/link.d "CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 82%] Built target gmxpreprocess-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f 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src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/checkpoint.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 82%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/mrcdensitymap.cpp [ 84%] Built target utility-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -MF CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o.d -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_memory.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/interactiveMD.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 84%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/minimize.cpp.o -MF CMakeFiles/minimize-test.dir/minimize.cpp.o.d -o CMakeFiles/minimize-test.dir/minimize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 84%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 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/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/xvgio.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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/usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 84%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -MF CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 84%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisim.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 85%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fileio-test.dir/link.d "CMakeFiles/fileio-test.dir/checkpoint.cpp.o" "CMakeFiles/fileio-test.dir/confio.cpp.o" "CMakeFiles/fileio-test.dir/filemd5.cpp.o" "CMakeFiles/fileio-test.dir/filetypes.cpp.o" "CMakeFiles/fileio-test.dir/mrcserializer.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o" "CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o" "CMakeFiles/fileio-test.dir/readinp.cpp.o" "CMakeFiles/fileio-test.dir/timecontrol.cpp.o" "CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o" "CMakeFiles/fileio-test.dir/tngio.cpp.o" "CMakeFiles/fileio-test.dir/xvgio.cpp.o" "CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target fileio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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-c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-mpi-test.dir/link.d "CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 86%] Built target mdrun-mpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 88%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisimtest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_coupling.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 89%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 89%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 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make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include 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../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target mdrun-non-integrator-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow/tests/workflow.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -MF CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o.d -o CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_constraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/runner.cpp.o -MF CMakeFiles/gmxapi-test.dir/runner.cpp.o.d -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/runner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-coupling-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 90%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake 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../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target workflow-details-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-fep-test.dir/link.d "CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o" "CMakeFiles/mdrun-fep-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-fep-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target mdrun-fep-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -MF CMakeFiles/nblib-setup-test.dir/interactions.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-constraints-test.dir/link.d "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/periodicactions_constraints.cpp.o" "CMakeFiles/mdrun-coordination-constraints-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-constraints-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target mdrun-coordination-constraints-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/bondtypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-rotation-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-basic-test.dir/link.d "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions_basic.cpp.o" "CMakeFiles/mdrun-coordination-basic-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-basic-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target mdrun-coordination-basic-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/gmxcalculator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-simulator-comparison-test.dir/link.txt --verbose=1 [ 92%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/setup.cpp.o -MF CMakeFiles/nblib-util-test.dir/setup.cpp.o.d -o CMakeFiles/nblib-util-test.dir/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests/setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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'/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/helpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target mdrun-vsites-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-tpr-test.dir/link.d "CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o" "CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-tpr-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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-c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 92%] Built target nblib-integrator-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-pull-test.dir/link.d "CMakeFiles/mdrun-pull-test.dir/pull.cpp.o" "CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-pull-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target mdrun-pull-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -MF CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/pbcholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target nblib-util-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-mpi-test.dir/link.d "CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o" "CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 93%] Built target mdrunutility-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -MF CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbnxmsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/kernels.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrunutility-test.dir/link.d "CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o" "CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o" "CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 94%] Built target mdrunutility-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/typetests.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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-I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now 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api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" 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-isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/average.cpp.o -MF CMakeFiles/analysisdata-test.dir/average.cpp.o.d -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c 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../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 94%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/hbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/msd.cpp cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 94%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 96%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 96%] Built target nblib-tests /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 97%] Built target commandline-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 98%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/basic-dp/lib ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/basic-dp/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2024.4/build/basic-dp Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1744828175 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 11 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.084 0.042 199.8 1: (ns/day) (hour/ns) 1: Performance: 12.008 1.999 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1255 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -118524097 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 12 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.102 0.051 199.7 1: (ns/day) (hour/ns) 1: Performance: 9.956 2.411 1: [ OK ] GmxApiTest.RunnerBasicMD (1487 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to 2147214840 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.506 0.253 199.9 1: (ns/day) (hour/ns) 1: Performance: 14.008 1.713 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.407 0.204 199.9 1: (ns/day) (hour/ns) 1: Performance: 17.398 1.379 1: [ OK ] GmxApiTest.RunnerReinitialize (1872 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to 1473511129 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 12 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.093 0.046 199.6 1: (ns/day) (hour/ns) 1: Performance: 10.901 2.202 1: trr version: GMX_trn_file (double precision) 1: 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 25, rlist from 1.062 to 1.197 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: NOTE: 25 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.073 0.037 199.7 1: (ns/day) (hour/ns) 1: Performance: 13.855 1.732 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (1233 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -275515525 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.145 0.073 199.8 1: (ns/day) (hour/ns) 1: Performance: 11.601 2.069 1: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.062 to 1 1: 1: 1: Using 1 MPI thread 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: NOTE: 12 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.044 0.022 199.5 1: (ns/day) (hour/ns) 1: Performance: 15.430 1.555 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (1115 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -825493 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (869 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (7833 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (7877 ms total) 1: [ PASSED ] 9 tests. 1/87 Test #1: GmxapiExternalInterfaceTests .............. Passed 8.00 sec test 2 Start 2: GmxapiInternalInterfaceTests 2: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests 2: Test timeout computed to be: 600 2: [==========] Running 2 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 2 tests from GmxApiTest 2: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to -1090560405 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.BuildApiWorkflowImpl (1038 ms) 2: [ RUN ] GmxApiTest.CreateApiWorkflow 2: Generating 1-4 interactions: fudge = 0.5 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Setting the LD random seed to 2147453822 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.CreateApiWorkflow (874 ms) 2: [----------] 2 tests from GmxApiTest (1929 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 2 tests from 1 test suite ran. (1965 ms total) 2: [ PASSED ] 2 tests. 2/87 Test #2: GmxapiInternalInterfaceTests .............. Passed 2.05 sec test 3 Start 3: NbLibListedForcesTests 3: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibListedForcesTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/listed_forces/tests 3: Test timeout computed to be: 600 3: [==========] Running 44 tests from 22 test suites. 3: [----------] Global test environment set-up. 3: [----------] 8 tests from NBlibTest 3: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 3: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 3: [ RUN ] NBlibTest.BondTypesLessThanWorks 3: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 3: [ RUN ] NBlibTest.CanSplitListedWork 3: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 3: [ RUN ] NBlibTest.ListedForceBuffer 3: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 3: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 3: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 3: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 3: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (0 ms) 3: [ RUN ] NBlibTest.EndToEndListedComparison 3: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 3: [ RUN ] NBlibTest.shiftForcesAreCorrect 3: [ OK ] NBlibTest.shiftForcesAreCorrect (48 ms) 3: [----------] 8 tests from NBlibTest (50 ms total) 3: 3: [----------] 1 test from Kernels 3: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 3: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 3: [----------] 1 test from Kernels (0 ms total) 3: 3: [----------] 1 test from FourCenter 3: [ RUN ] FourCenter.ListedForcesProperDihedralTest 3: [ OK ] FourCenter.ListedForcesProperDihedralTest (4 ms) 3: [----------] 1 test from FourCenter (4 ms total) 3: 3: [----------] 7 tests from ThreeCenter 3: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 3: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 3: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 3: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 3: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 3: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 3: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 3: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 3: [----------] 7 tests from ThreeCenter (0 ms total) 3: 3: [----------] 5 tests from TwoCenter 3: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 3: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesG96BondTest 3: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesCubicBondTest 3: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesMorseBondTest 3: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 3: [ RUN ] TwoCenter.ListedForcesFeneBondTest 3: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 3: [----------] 5 tests from TwoCenter (0 ms total) 3: 3: [----------] 5 tests from ListedExampleData 3: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 3: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 3: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 3: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 3: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceForces 3: [ OK ] ListedExampleData.CanReduceForces (0 ms) 3: [ RUN ] ListedExampleData.CanReduceEnergies 3: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 3: [----------] 5 tests from ListedExampleData (0 ms total) 3: 3: [----------] 1 test from LinearChainDataFixture 3: [ RUN ] LinearChainDataFixture.Multithreading 3: [ OK ] LinearChainDataFixture.Multithreading (43 ms) 3: [----------] 1 test from LinearChainDataFixture (43 ms total) 3: 3: [----------] 2 tests from ListedShims 3: [ RUN ] ListedShims.ParameterConversion 3: [ OK ] ListedShims.ParameterConversion (0 ms) 3: [ RUN ] ListedShims.GmxToNblibConversion 3: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 3: [----------] 2 tests from ListedShims (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 3: 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 3: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 3: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 3: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 3: 3: [----------] 1 test from ListedTransformations 3: [ RUN ] ListedTransformations.SortInteractionIndices 3: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 3: [----------] 1 test from ListedTransformations (0 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 44 tests from 22 test suites ran. (99 ms total) 3: [ PASSED ] 44 tests. 3/87 Test #3: NbLibListedForcesTests .................... Passed 0.16 sec test 4 Start 4: NbLibSamplesTestArgon 4: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/argon-forces-integration 4: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples 4: Test timeout computed to be: 1500 4: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 4: final forces on particle 0: x -0.412988 y -1.098243 z -0.113189 4: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 4: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 4/87 Test #4: NbLibSamplesTestArgon ..................... Passed 0.07 sec test 5 Start 5: NbLibSamplesTestMethaneWater 5: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/methane-water-integration 5: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/samples 5: Test timeout computed to be: 1500 5: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 5: final position of particle 9: x 77.358372 y 5.325207 z -80.600064 5/87 Test #5: NbLibSamplesTestMethaneWater .............. Passed 0.13 sec test 6 Start 6: NbLibUtilTests 6: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibUtilTests.xml" 6: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/util/tests 6: Test timeout computed to be: 30 6: [==========] Running 16 tests from 2 test suites. 6: [----------] Global test environment set-up. 6: [----------] 6 tests from NBlibTest 6: [ RUN ] NBlibTest.isRealValued 6: [ OK ] NBlibTest.isRealValued (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasNan 6: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 6: [ RUN ] NBlibTest.checkNumericValuesHasInf 6: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 6: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 6: [ RUN ] NBlibTest.generateVelocitySize 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocitySize (0 ms) 6: [ RUN ] NBlibTest.generateVelocityCheckNumbers 6: Velocities were taken from a Maxwell distribution at 300 K 6: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 6: [----------] 6 tests from NBlibTest (0 ms total) 6: 6: [----------] 10 tests from NblibTraitsUtils 6: [ RUN ] NblibTraitsUtils.FuseTwo 6: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 6: [ RUN ] NblibTraitsUtils.Fuse 6: [ OK ] NblibTraitsUtils.Fuse (0 ms) 6: [ RUN ] NblibTraitsUtils.Repeat 6: [ OK ] NblibTraitsUtils.Repeat (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple1 6: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTuple2 6: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 6: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 6: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 6: [ RUN ] NblibTraitsUtils.Contains 6: [ OK ] NblibTraitsUtils.Contains (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 6: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 6: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 6: [----------] 10 tests from NblibTraitsUtils (0 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 16 tests from 2 test suites ran. (16 ms total) 6: [ PASSED ] 16 tests. 6/87 Test #6: NbLibUtilTests ............................ Passed 0.06 sec test 7 Start 7: NbLibSetupTests 7: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibSetupTests.xml" 7: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests 7: Test timeout computed to be: 600 7: [==========] Running 57 tests from 3 test suites. 7: [----------] Global test environment set-up. 7: [----------] 41 tests from NBlibTest 7: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 7: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 7: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 7: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 7: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 7: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 7: [ RUN ] NBlibTest.CubicBoxWorks 7: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 7: [ RUN ] NBlibTest.BoxEqual 7: [ OK ] NBlibTest.BoxEqual (0 ms) 7: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 7: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 7: [ RUN ] NBlibTest.CanMergeInteractions 7: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 7: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 7: [ RUN ] NBlibTest.PbcHolderWorks 7: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 7: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 7: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 7: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 7: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 7: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 7: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 7: [ RUN ] NBlibTest.AtWorks 7: [ OK ] NBlibTest.AtWorks (0 ms) 7: [ RUN ] NBlibTest.AtThrows 7: [ OK ] NBlibTest.AtThrows (0 ms) 7: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 7: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 7: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 7: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 7: [ RUN ] NBlibTest.CanAddInteractions 7: [ OK ] NBlibTest.CanAddInteractions (0 ms) 7: [ RUN ] NBlibTest.CanAddUreyBradley 7: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 7: [ RUN ] NBlibTest.TopologyHasNumParticles 7: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 7: [ RUN ] NBlibTest.TopologyHasCharges 7: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 7: [ RUN ] NBlibTest.TopologyHasMasses 7: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypes 7: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 7: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 7: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 7: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 7: [ RUN ] NBlibTest.TopologyHasExclusions 7: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 7: [ RUN ] NBlibTest.TopologyHasSequencing 7: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 7: [ RUN ] NBlibTest.TopologyCanAggregateBonds 7: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 7: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 7: [ RUN ] NBlibTest.TopologySequenceIdThrows 7: No particle O-Atom in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 7: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 7: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractions 7: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 7: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 7: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 7: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 7: No particle Iron in residue SOL in molecule SOL found 7: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 7: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 7: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 7: [----------] 41 tests from NBlibTest (10 ms total) 7: 7: [----------] 15 tests from NbnxmSetupTest 7: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 7: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 7: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 7: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 7: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 7: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 7: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 7: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 7: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 7: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.updateForcerecWorks 7: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 7: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 7: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 7: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 7: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 7: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 7: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 7: [----------] 15 tests from NbnxmSetupTest (0 ms total) 7: 7: [----------] 1 test from VirialsTest 7: [ RUN ] VirialsTest.computeVirialTensorWorks 7: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 7: [----------] 1 test from VirialsTest (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 57 tests from 3 test suites ran. (11 ms total) 7: [ PASSED ] 57 tests. 7/87 Test #7: NbLibSetupTests ........................... Passed 0.09 sec test 8 Start 8: NbLibTprTests 8: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibTprTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests 8: Test timeout computed to be: 30 8: [==========] Running 4 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 4 tests from TprReaderTest 8: [ RUN ] TprReaderTest.SimDBTprIsCreated 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.SimDBTprIsCreated (27 ms) 8: [ RUN ] TprReaderTest.Spc2Reads 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Generating 1-4 interactions: fudge = 0.5 8: Number of degrees of freedom in T-Coupling group System is 9.00 8: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: NVE simulation: will use the initial temperature of 2573.591 K for 8: determining the Verlet buffer size 8: 8: 8: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 8: You are using a plain Coulomb cut-off, which might produce artifacts. 8: You might want to consider using PME electrostatics. 8: 8: 8: 8: There were 4 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 8: Generated 3 of the 3 non-bonded parameter combinations 8: 8: Generated 3 of the 3 1-4 parameter combinations 8: 8: Excluding 2 bonded neighbours molecule type 'SOL' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.Spc2Reads (15 ms) 8: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (16 ms) 8: [ RUN ] TprReaderTest.FCfromTprDataWorks 8: 8: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 8: that with the Verlet scheme, nstlist has no effect on the accuracy of 8: your simulation. 8: 8: 8: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: Setting nstcalcenergy (100) equal to nstenergy (4) 8: 8: Number of degrees of freedom in T-Coupling group System is 33.00 8: 8: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 8: NVE simulation: will use the initial temperature of 68.810 K for 8: determining the Verlet buffer size 8: 8: 8: There were 3 NOTEs 8: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 8: Generated 1 of the 1 non-bonded parameter combinations 8: 8: Excluding 1 bonded neighbours molecule type 'Argon' 8: 8: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 8: 8: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 8: 8: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 8: 8: Note that mdrun will redetermine rlist based on the actual pair-list setup 8: 8: This run will generate roughly 0 Mb of data 8: [ OK ] TprReaderTest.FCfromTprDataWorks (16 ms) 8: [----------] 4 tests from TprReaderTest (76 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 4 tests from 1 test suite ran. (120 ms total) 8: [ PASSED ] 4 tests. 8/87 Test #8: NbLibTprTests ............................. Passed 0.23 sec test 9 Start 9: NbLibIntegrationTests 9: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibIntegrationTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 20 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 20 tests from NBlibTest 9: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 9: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (8 ms) 9: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 9: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 9: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 9: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ExpectedNumberOfForces 9: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 9: [ RUN ] NBlibTest.CanIntegrateSystem 9: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 9: [ RUN ] NBlibTest.UpdateChangesForces 9: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 9: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 9: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 9: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (0 ms) 9: [ RUN ] NBlibTest.CanConstructSimulationState 9: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 9: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 9: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 9: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanMove 9: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 9: [ RUN ] NBlibTest.SimulationStateCanAssign 9: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasBox 9: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 9: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 9: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 9: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 9: [----------] 20 tests from NBlibTest (11 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 20 tests from 1 test suite ran. (11 ms total) 9: [ PASSED ] 20 tests. 9/87 Test #9: NbLibIntegrationTests ..................... Passed 0.06 sec test 10 Start 10: NbLibIntegratorTests 10: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbLibIntegratorTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib/tests 10: Test timeout computed to be: 600 10: [==========] Running 1 test from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 1 test from NBlibTest 10: [ RUN ] NBlibTest.IntegratorWorks 10: [ OK ] NBlibTest.IntegratorWorks (0 ms) 10: [----------] 1 test from NBlibTest (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 1 test from 1 test suite ran. (0 ms total) 10: [ PASSED ] 1 test. 10/87 Test #10: NbLibIntegratorTests ...................... Passed 0.06 sec test 11 Start 11: TestUtilsUnitTests 11: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests 11: Test timeout computed to be: 30 11: [==========] Running 59 tests from 5 test suites. 11: [----------] Global test environment set-up. 11: [----------] 10 tests from InteractiveTestHelperTest 11: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 11: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 11: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 11: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 11: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 11: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 11: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 11: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 11: 11: [----------] 34 tests from ReferenceDataTest 11: [ RUN ] ReferenceDataTest.HandlesSimpleData 11: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 11: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 11: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringBlockData 11: [ OK ] ReferenceDataTest.HandlesStringBlockData (12 ms) 11: [ RUN ] ReferenceDataTest.HandlesVectorData 11: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceData 11: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 11: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectData 11: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 11: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingData 11: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedData 11: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 11: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnys 11: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 11: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 11: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 11: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 11: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 11: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 11: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 11: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 11: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 11: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 11: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 11: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesReadingValues 11: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 11: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 11: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 11: [----------] 34 tests from ReferenceDataTest (14 ms total) 11: 11: [----------] 7 tests from FloatingPointDifferenceTest 11: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 11: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 11: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 11: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 11: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 11: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 11: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 11: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 11: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 11: 11: [----------] 4 tests from FloatingPointToleranceTest 11: [ RUN ] FloatingPointToleranceTest.UlpTolerance 11: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 11: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 11: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 11: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 11: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 11: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 11: 11: [----------] 4 tests from XvgTests 11: [ RUN ] XvgTests.CreateFile 11: [ OK ] XvgTests.CreateFile (0 ms) 11: [ RUN ] XvgTests.CheckMissing 11: [ OK ] XvgTests.CheckMissing (0 ms) 11: [ RUN ] XvgTests.CheckExtra 11: [ OK ] XvgTests.CheckExtra (0 ms) 11: [ RUN ] XvgTests.ReadIncorrect 11: [ OK ] XvgTests.ReadIncorrect (0 ms) 11: [----------] 4 tests from XvgTests (0 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 59 tests from 5 test suites ran. (16 ms total) 11: [ PASSED ] 59 tests. 11/87 Test #11: TestUtilsUnitTests ........................ Passed 0.07 sec test 12 Start 12: TestUtilsMpiUnitTests 12: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/testutils/tests 12: Test timeout computed to be: 30 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from MpiSelfTest 12: [ RUN ] MpiSelfTest.Runs 12: [ OK ] MpiSelfTest.Runs (65 ms) 12: [----------] 1 test from MpiSelfTest (65 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (65 ms total) 12: [ PASSED ] 1 test. 12/87 Test #12: TestUtilsMpiUnitTests ..................... Passed 0.14 sec test 13 Start 13: UtilityUnitTests 13: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests 13: Test timeout computed to be: 30 13: [==========] Running 400 tests from 62 test suites. 13: [----------] Global test environment set-up. 13: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/0.Move 13: [ OK ] AllocatorTest/0.Move (0 ms) 13: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/0 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/1.Move 13: [ OK ] AllocatorTest/1.Move (0 ms) 13: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/1 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/2.Move 13: [ OK ] AllocatorTest/2.Move (0 ms) 13: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/2 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 13: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/3.Move 13: [ OK ] AllocatorTest/3.Move (0 ms) 13: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/3 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/4.Move 13: [ OK ] AllocatorTest/4.Move (0 ms) 13: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/4 (0 ms total) 13: 13: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 13: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 13: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 13: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 13: [ RUN ] AllocatorTest/5.Move 13: [ OK ] AllocatorTest/5.Move (0 ms) 13: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 13: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 13: [----------] 5 tests from AllocatorTest/5 (0 ms total) 13: 13: [----------] 1 test from AllocatorUntypedTest 13: [ RUN ] AllocatorUntypedTest.Comparison 13: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 13: [----------] 1 test from AllocatorUntypedTest (0 ms total) 13: 13: [----------] 4 tests from EmptyArrayRefTest 13: [ RUN ] EmptyArrayRefTest.IsEmpty 13: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 13: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 13: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 13: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 13: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 13: 13: [----------] 1 test from EmptyConstArrayRefTest 13: [ RUN ] EmptyConstArrayRefTest.IsEmpty 13: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 13: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 13: 13: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 13: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 13: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 13: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 13: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 13: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 13: 13: [----------] 8 tests from BoolType 13: [ RUN ] BoolType.ImplicitConversion 13: [ OK ] BoolType.ImplicitConversion (0 ms) 13: [ RUN ] BoolType.FalseByDefault 13: [ OK ] BoolType.FalseByDefault (0 ms) 13: [ RUN ] BoolType.Assignment 13: [ OK ] BoolType.Assignment (0 ms) 13: [ RUN ] BoolType.Copy 13: [ OK ] BoolType.Copy (0 ms) 13: [ RUN ] BoolType.ArrayRefCanBeCreated 13: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 13: [ RUN ] BoolType.CanBeCastToBool 13: [ OK ] BoolType.CanBeCastToBool (0 ms) 13: [ RUN ] BoolType.HasSizeOfBool 13: [ OK ] BoolType.HasSizeOfBool (0 ms) 13: [ RUN ] BoolType.HasAlignmentOfBool 13: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 13: [----------] 8 tests from BoolType (0 ms total) 13: 13: [----------] 4 tests from ArrayRefFromBoolTypeVector 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.Works 13: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 13: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 13: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 13: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 13: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 13: 13: [----------] 7 tests from CStringUtilityTest 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 13: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 13: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 13: [ RUN ] CStringUtilityTest.strip_comment 13: [ OK ] CStringUtilityTest.strip_comment (0 ms) 13: [ RUN ] CStringUtilityTest.upstring 13: [ OK ] CStringUtilityTest.upstring (0 ms) 13: [ RUN ] CStringUtilityTest.ltrim 13: [ OK ] CStringUtilityTest.ltrim (0 ms) 13: [ RUN ] CStringUtilityTest.rtrim 13: [ OK ] CStringUtilityTest.rtrim (0 ms) 13: [ RUN ] CStringUtilityTest.trim 13: [ OK ] CStringUtilityTest.trim (0 ms) 13: [----------] 7 tests from CStringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from DefaultInitializationAllocator 13: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 13: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 13: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 13: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 13: 13: [----------] 4 tests from EnumerationHelpersTest 13: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 13: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 13: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 13: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 13: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 13: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 13: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 13: 13: [----------] 9 tests from FixedCapacityVectorTest 13: [ RUN ] FixedCapacityVectorTest.IsEmpty 13: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PushWorks 13: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.PopWorks 13: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ClearWorks 13: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 13: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.AtThrows 13: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 13: [ RUN ] FixedCapacityVectorTest.IteratorWorks 13: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 13: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 13: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 13: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 13: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 13: 13: [----------] 5 tests from InMemorySerializerTest 13: [ RUN ] InMemorySerializerTest.Roundtrip 13: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 13: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 13: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 13: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 13: [ RUN ] InMemorySerializerTest.SizeIsCorrect 13: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 13: [----------] 5 tests from InMemorySerializerTest (0 ms total) 13: 13: [----------] 4 tests from KeyValueTreeSerializerTest 13: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 13: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 13: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (20 ms) 13: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 13: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 13: [----------] 4 tests from KeyValueTreeSerializerTest (20 ms total) 13: 13: [----------] 7 tests from TreeValueTransformTest 13: [ RUN ] TreeValueTransformTest.SimpleTransforms 13: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 13: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 13: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 13: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromString 13: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 13: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 13: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 13: [ RUN ] TreeValueTransformTest.ScopedTransformRules 13: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 13: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 13: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 13: [----------] 7 tests from TreeValueTransformTest (0 ms total) 13: 13: [----------] 1 test from TreeValueTransformErrorTest 13: [ RUN ] TreeValueTransformErrorTest.ConversionError 13: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 13: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 13: 13: [----------] 9 tests from ListOfLists 13: [ RUN ] ListOfLists.EmptyListOfListsWorks 13: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 13: [ RUN ] ListOfLists.AppendWorks 13: [ OK ] ListOfLists.AppendWorks (0 ms) 13: [ RUN ] ListOfLists.EmptyListWorks 13: [ OK ] ListOfLists.EmptyListWorks (0 ms) 13: [ RUN ] ListOfLists.AppendAccessWorks 13: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 13: [ RUN ] ListOfLists.ClearWorks 13: [ OK ] ListOfLists.ClearWorks (0 ms) 13: [ RUN ] ListOfLists.OutOfRangeAccessThrows 13: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 13: [ RUN ] ListOfLists.FrontAndBackWork 13: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 13: [ RUN ] ListOfLists.ExtractsAndRestores 13: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 13: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 13: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 13: [----------] 9 tests from ListOfLists (0 ms total) 13: 13: [----------] 7 tests from LoggerTest 13: [ RUN ] LoggerTest.EmptyLoggerWorks 13: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToStream 13: [ OK ] LoggerTest.LogsToStream (0 ms) 13: [ RUN ] LoggerTest.LogsToFile 13: [ OK ] LoggerTest.LogsToFile (0 ms) 13: [ RUN ] LoggerTest.LevelFilteringWorks 13: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleStreams 13: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 13: [ RUN ] LoggerTest.LogsToMultipleFiles 13: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 13: [ RUN ] LoggerTest.LogsToStreamAndFile 13: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 13: [----------] 7 tests from LoggerTest (0 ms total) 13: 13: [----------] 7 tests from MessageStringCollectorTest 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 13: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 13: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 13: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 13: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 13: [ RUN ] MessageStringCollectorTest.CanMoveAssign 13: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 13: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 13: 13: [----------] 1 test from PathTest 13: [ RUN ] PathTest.StripSourcePrefixWorks 13: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 13: [----------] 1 test from PathTest (0 ms total) 13: 13: [----------] 2 tests from PhysicalNodeCommunicatorTest 13: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 13: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 13: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 13: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 13: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 13: 13: [----------] 5 tests from Range 13: [ RUN ] Range.EmptyRangeWorks 13: [ OK ] Range.EmptyRangeWorks (0 ms) 13: [ RUN ] Range.NonEmptyRangeWorks 13: [ OK ] Range.NonEmptyRangeWorks (0 ms) 13: [ RUN ] Range.BeginEnd 13: [ OK ] Range.BeginEnd (0 ms) 13: [ RUN ] Range.IsInRangeWorks 13: [ OK ] Range.IsInRangeWorks (0 ms) 13: [ RUN ] Range.IteratorWorks 13: [ OK ] Range.IteratorWorks (0 ms) 13: [----------] 5 tests from Range (0 ms total) 13: 13: [----------] 7 tests from StringConvert 13: [ RUN ] StringConvert.NoResultFromEptyString 13: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 13: [ RUN ] StringConvert.ThreeFloatsSuccessfully 13: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 13: [ RUN ] StringConvert.OneIntSucessfully 13: [ OK ] StringConvert.OneIntSucessfully (0 ms) 13: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 13: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 13: [ RUN ] StringConvert.ThrowsWhenWrongSize 13: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 13: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 13: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 13: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 13: [----------] 7 tests from StringConvert (0 ms total) 13: 13: [----------] 7 tests from StringToEnumValueConverterTest 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 13: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 13: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 13: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 13: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 13: 13: [----------] 9 tests from StringUtilityTest 13: [ RUN ] StringUtilityTest.StartsWith 13: [ OK ] StringUtilityTest.StartsWith (0 ms) 13: [ RUN ] StringUtilityTest.EndsWith 13: [ OK ] StringUtilityTest.EndsWith (0 ms) 13: [ RUN ] StringUtilityTest.StripSuffixIfPresent 13: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 13: [ RUN ] StringUtilityTest.StripString 13: [ OK ] StringUtilityTest.StripString (0 ms) 13: [ RUN ] StringUtilityTest.SplitString 13: [ OK ] StringUtilityTest.SplitString (0 ms) 13: [ RUN ] StringUtilityTest.SplitDelimitedString 13: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 13: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 13: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 13: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 13: [----------] 9 tests from StringUtilityTest (0 ms total) 13: 13: [----------] 2 tests from FormatStringTest 13: [ RUN ] FormatStringTest.HandlesBasicFormatting 13: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 13: [ RUN ] FormatStringTest.HandlesLongStrings 13: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 13: [----------] 2 tests from FormatStringTest (0 ms total) 13: 13: [----------] 1 test from StringFormatterTest 13: [ RUN ] StringFormatterTest.HandlesBasicFormatting 13: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 13: [----------] 1 test from StringFormatterTest (0 ms total) 13: 13: [----------] 1 test from formatAndJoinTest 13: [ RUN ] formatAndJoinTest.Works 13: [ OK ] formatAndJoinTest.Works (0 ms) 13: [----------] 1 test from formatAndJoinTest (0 ms total) 13: 13: [----------] 1 test from JoinStringsTest 13: [ RUN ] JoinStringsTest.Works 13: [ OK ] JoinStringsTest.Works (0 ms) 13: [----------] 1 test from JoinStringsTest (0 ms total) 13: 13: [----------] 6 tests from ReplaceAllTest 13: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 13: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesNoMatches 13: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 13: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 13: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 13: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 13: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 13: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 13: [----------] 6 tests from ReplaceAllTest (0 ms total) 13: 13: [----------] 10 tests from TextLineWrapperTest 13: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 13: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 13: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 13: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectly 13: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndent 13: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 13: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 13: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 13: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 13: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 13: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 13: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 13: [----------] 10 tests from TextLineWrapperTest (0 ms total) 13: 13: [----------] 3 tests from TemplateMPTest 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 13: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 13: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 13: [----------] 3 tests from TemplateMPTest (0 ms total) 13: 13: [----------] 6 tests from TextWriterTest 13: [ RUN ] TextWriterTest.WritesLines 13: [ OK ] TextWriterTest.WritesLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInParts 13: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 13: [ RUN ] TextWriterTest.WritesWrappedLines 13: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 13: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 13: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 13: [ RUN ] TextWriterTest.TracksNewlines 13: [ OK ] TextWriterTest.TracksNewlines (0 ms) 13: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 13: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 13: [----------] 6 tests from TextWriterTest (0 ms total) 13: 13: [----------] 1 test from TypeTraitsTest 13: [ RUN ] TypeTraitsTest.IsIntegralConstant 13: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 13: [----------] 1 test from TypeTraitsTest (0 ms total) 13: 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 13: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 13: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 13: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 13: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 13: 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 13: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 13: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 13: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 13: 13: [----------] 11 tests from WithInputPaths/PathSearchTest 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 13: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 13: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 13: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 13: 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 13: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 13: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 13: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 400 tests from 62 test suites ran. (25 ms total) 13: [ PASSED ] 400 tests. 13: 13: YOU HAVE 1 DISABLED TEST 13: 13/87 Test #13: UtilityUnitTests .......................... Passed 0.11 sec test 14 Start 14: UtilityMpiUnitTests 14: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/utility-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/utility/tests 14: Test timeout computed to be: 30 14: [==========] Running 2 tests from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 2 tests from PhysicalNodeCommunicatorTest 14: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 14: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (14 ms) 14: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 14: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (23 ms) 14: [----------] 2 tests from PhysicalNodeCommunicatorTest (38 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 2 tests from 1 test suite ran. (38 ms total) 14: [ PASSED ] 2 tests. 14/87 Test #14: UtilityMpiUnitTests ....................... Passed 0.11 sec test 15 Start 15: GmxlibTests 15: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxlibTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxlib/nonbonded/tests 15: Test timeout computed to be: 30 15: [==========] Running 78 tests from 2 test suites. 15: [----------] Global test environment set-up. 15: [----------] 72 tests from NBInteraction/NonbondedFepTest 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (8 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (16 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 15: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 15: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 15: [----------] 72 tests from NBInteraction/NonbondedFepTest (30 ms total) 15: 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 15: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 15: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 15: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 78 tests from 2 test suites ran. (30 ms total) 15: [ PASSED ] 78 tests. 15/87 Test #15: GmxlibTests ............................... Passed 0.10 sec test 16 Start 16: MdlibUnitTest 16: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 16: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests 16: Test timeout computed to be: 30 16: [==========] Running 999 tests from 25 test suites. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from EffectiveAtomDensity 16: [ RUN ] EffectiveAtomDensity.VolumeIndependence 16: [ OK ] EffectiveAtomDensity.VolumeIndependence (0 ms) 16: [ RUN ] EffectiveAtomDensity.WeightingWorks 16: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 16: [----------] 2 tests from EffectiveAtomDensity (0 ms total) 16: 16: [----------] 2 tests from AtomNonbondedAndKineticProperties 16: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 16: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 16: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 16: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 16: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 16: 16: [----------] 1 test from VerletBufferConstraintTest 16: [ RUN ] VerletBufferConstraintTest.EqualMasses 16: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 16: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 16: 16: [----------] 6 tests from CalcvirTest 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 16: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (0 ms) 16: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 16: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 16: [----------] 6 tests from CalcvirTest (0 ms total) 16: 16: [----------] 2 tests from PrEbinTest 16: [ RUN ] PrEbinTest.HandlesAverages 16: [ OK ] PrEbinTest.HandlesAverages (0 ms) 16: [ RUN ] PrEbinTest.HandlesEmptyAverages 16: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 16: [----------] 2 tests from PrEbinTest (0 ms total) 16: 16: [----------] 3 tests from EnergyDriftTracker 16: [ RUN ] EnergyDriftTracker.emptyWorks 16: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.onePointWorks 16: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 16: [ RUN ] EnergyDriftTracker.manyPointsWorks 16: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 16: [----------] 3 tests from EnergyDriftTracker (0 ms total) 16: 16: [----------] 4 tests from ShakeTest 16: [ RUN ] ShakeTest.ConstrainsOneBond 16: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 16: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 16: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 16: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 16: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 16: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 16: [----------] 4 tests from ShakeTest (0 ms total) 16: 16: [----------] 1 test from NullSignalTest 16: [ RUN ] NullSignalTest.NullSignallerWorks 16: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 16: [----------] 1 test from NullSignalTest (0 ms total) 16: 16: [----------] 7 tests from SignalTest 16: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 16: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 16: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 16: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 16: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 16: [----------] 7 tests from SignalTest (0 ms total) 16: 16: [----------] 13 tests from UpdateGroupsTest 16: [ RUN ] UpdateGroupsTest.WithEthaneUA 16: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 16: [ RUN ] UpdateGroupsTest.WithMethane 16: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithEthane 16: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 16: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 16: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 16: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFourSite 16: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 16: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 16: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 16: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 16: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 16: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 16: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 16: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 16: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 16: [----------] 13 tests from UpdateGroupsTest (0 ms total) 16: 16: [----------] 1 test from UpdateGroupsCog 16: [ RUN ] UpdateGroupsCog.ComputesCogs 16: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 16: [----------] 1 test from UpdateGroupsCog (0 ms total) 16: 16: [----------] 2 tests from WholeMoleculeTransform 16: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 16: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 16: [ RUN ] WholeMoleculeTransform.HandlesReordering 16: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 16: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 16: 16: [----------] 14 tests from WithParameters/ConstraintsTest 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (12 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (31 ms) 16: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 16: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (23 ms) 16: [----------] 14 tests from WithParameters/ConstraintsTest (69 ms total) 16: 16: [----------] 11 tests from WithParameters/EnergyOutputTest 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (11 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 16: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file 16: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (24 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (1 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (0 ms) 16: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 16: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file 16: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 16: [----------] 11 tests from WithParameters/EnergyOutputTest (66 ms total) 16: 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (1 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 16: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 16: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 16: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (1 ms total) 16: 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 16: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 16: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 16: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 16: 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 16: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 16: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 16: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 16: 16: [----------] 16 tests from WithParameters/LeapFrogTest 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (11 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (21 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (5 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (11 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (1 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (5 ms) 16: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 16: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (1 ms) 16: [----------] 16 tests from WithParameters/LeapFrogTest (61 ms total) 16: 16: [----------] 140 tests from Cubic/ParrRahmTest 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (16 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (1 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 16: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 16: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Cubic/ParrRahmTest (21 ms total) 16: 16: [----------] 140 tests from Rectilinear/ParrRahmTest 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 16: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 16: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Rectilinear/ParrRahmTest (3 ms total) 16: 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (24 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 16: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (28 ms total) 16: 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (20 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (20 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 16: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 16: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (44 ms total) 16: 16: [----------] 140 tests from TruncOct/ParrRahmTest 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (12 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 16: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 16: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from TruncOct/ParrRahmTest (16 ms total) 16: 16: [----------] 140 tests from Other/ParrRahmTest 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (20 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 16: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 16: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 16: [----------] 140 tests from Other/ParrRahmTest (24 ms total) 16: 16: [----------] 13 tests from WithParameters/SettleTest 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (21 ms) 16: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 16: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 16: [----------] 13 tests from WithParameters/SettleTest (24 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 999 tests from 25 test suites ran. (363 ms total) 16: [ PASSED ] 999 tests. 16/87 Test #16: MdlibUnitTest ............................. Passed 0.77 sec test 17 Start 17: AwhTest 17: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/AwhTest.xml" 17: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/awh/tests 17: Test timeout computed to be: 30 17: [==========] Running 27 tests from 10 test suites. 17: [----------] Global test environment set-up. 17: [----------] 3 tests from SerializationTest 17: [ RUN ] SerializationTest.CanSerializeDimParams 17: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeBiasParams 17: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 17: [ RUN ] SerializationTest.CanSerializeAwhParams 17: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 17: [----------] 3 tests from SerializationTest (0 ms total) 17: 17: [----------] 1 test from BiasTest 17: [ RUN ] BiasTest.DetectsCovering 17: [ OK ] BiasTest.DetectsCovering (0 ms) 17: [----------] 1 test from BiasTest (0 ms total) 17: 17: [----------] 1 test from biasGridTest 17: [ RUN ] biasGridTest.neighborhood 17: [ OK ] biasGridTest.neighborhood (16 ms) 17: [----------] 1 test from biasGridTest (16 ms total) 17: 17: [----------] 2 tests from BiasSharingTest 17: [ RUN ] BiasSharingTest.SharingWorks 17: [ OK ] BiasSharingTest.SharingWorks (139 ms) 17: [ RUN ] BiasSharingTest.SharingScalingByMetricWorks 17: [ OK ] BiasSharingTest.SharingScalingByMetricWorks (1727 ms) 17: [----------] 2 tests from BiasSharingTest (1867 ms total) 17: 17: [----------] 2 tests from BiasFepLambdaStateTest 17: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 17: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 17: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 17: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 17: [----------] 2 tests from BiasFepLambdaStateTest (1 ms total) 17: 17: [----------] 8 tests from WithParameters/BiasTest 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (13 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 17: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 17: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 17: [----------] 8 tests from WithParameters/BiasTest (15 ms total) 17: 17: [----------] 2 tests from WithParameters/BiasStateTest 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 17: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 17: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 17: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 17: 17: [----------] 1 test from WithParameters/UserInputTest 17: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 17: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 17: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 17: 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (8 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (3 ms) 17: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 17: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (7 ms) 17: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (28 ms total) 17: 17: [----------] 3 tests from WithParameters/FrictionMetricTest 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (4 ms) 17: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 17: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (29 ms) 17: [----------] 3 tests from WithParameters/FrictionMetricTest (35 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 27 tests from 10 test suites ran. (1968 ms total) 17: [ PASSED ] 27 tests. 17/87 Test #17: AwhTest ................................... Passed 2.03 sec test 18 Start 18: DensityFittingAppliedForcesUnitTest 18: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/densityfitting/tests 18: Test timeout computed to be: 30 18: [==========] Running 18 tests from 4 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from DensityFittingTest 18: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 18: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 18: [ RUN ] DensityFittingTest.SingleAtom 18: [ OK ] DensityFittingTest.SingleAtom (0 ms) 18: [----------] 2 tests from DensityFittingTest (0 ms total) 18: 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest 18: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 18: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 18: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 18: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 18: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 18: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 18: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 18: 18: [----------] 1 test from DensityFittingForceProviderState 18: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 18: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 18: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 18: 18: [----------] 8 tests from DensityFittingOptionsTest 18: [ RUN ] DensityFittingOptionsTest.DefaultParameters 18: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 18: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 18: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 18: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 18: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 18: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 18: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 18: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 18: [ RUN ] DensityFittingOptionsTest.KvtToInternal 18: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 18: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 18: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 18: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 18 tests from 4 test suites ran. (1 ms total) 18: [ PASSED ] 18 tests. 18/87 Test #18: DensityFittingAppliedForcesUnitTest ....... Passed 0.04 sec test 19 Start 19: QMMMAppliedForcesUnitTest 19: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests 19: Test timeout computed to be: 30 19: [==========] Running 21 tests from 5 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from QMMMInputGeneratorTest 19: [ RUN ] QMMMInputGeneratorTest.CanConstruct 19: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 19: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 19: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 19: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 19: 19: [----------] 7 tests from QMMMTopologyPreprocessorTest 19: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 19: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -421691525 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (11 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -150997137 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (10 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 21.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -1174446609 19: 19: Generated 10 of the 10 non-bonded parameter combinations 19: 19: Generated 10 of the 10 1-4 parameter combinations 19: 19: Excluding 2 bonded neighbours molecule type 'SOL' 19: Analysing residue names: 19: There are: 4 Water residues 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: Number of degrees of freedom in T-Coupling group rest is 63.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 129.093 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -591407117 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (22 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Generating 1-4 interactions: fudge = 0.5 19: 19: NOTE 2 [file unknown]: 19: You are using constraints on all bonds, whereas the forcefield has been 19: parametrized only with constraints involving hydrogen atoms. We suggest 19: using constraints = h-bonds instead, this will also improve performance. 19: 19: 19: NOTE 3 [file unknown]: 19: For energy conservation with LINCS, lincs_iter should be 2 or larger. 19: 19: 19: Number of degrees of freedom in T-Coupling group rest is 42.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: NVE simulation: will use the initial temperature of 193.640 K for 19: determining the Verlet buffer size 19: 19: 19: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 5 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -10497 19: 19: Generated 2145 of the 2145 non-bonded parameter combinations 19: 19: Generated 2145 of the 2145 1-4 parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 19: 19: turning all bonds into constraints... 19: Analysing residue names: 19: There are: 3 Protein residues 19: Analysing Protein... 19: 19: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 19: 19: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 19: 19: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 19: 19: Note that mdrun will redetermine rlist based on the actual pair-list setup 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (9 ms) 19: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 19: 19: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: For a correct single-point energy evaluation with nsteps = 0, use 19: continuation = yes to avoid constraining the input coordinates. 19: 19: Number of degrees of freedom in T-Coupling group rest is 45.00 19: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 19: 19: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: NVE simulation with an initial temperature of zero: will use a Verlet 19: buffer of 10%. Check your energy drift! 19: 19: 19: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 19: You are using a plain Coulomb cut-off, which might produce artifacts. 19: You might want to consider using PME electrostatics. 19: 19: 19: 19: There were 3 NOTEs 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 19: Setting the LD random seed to -537346053 19: 19: Generated 3 of the 6 non-bonded parameter combinations 19: 19: Excluding 3 bonded neighbours molecule type 'VSTEST' 19: 19: Cleaning up constraints and constant bonded interactions with virtual sites 19: Analysing residue names: 19: There are: 1 Other residues 19: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 19: 19: This run will generate roughly 0 Mb of data 19: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (14 ms) 19: [----------] 7 tests from QMMMTopologyPreprocessorTest (71 ms total) 19: 19: [----------] 9 tests from QMMMOptionsTest 19: [ RUN ] QMMMOptionsTest.DefaultParameters 19: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 19: [ RUN ] QMMMOptionsTest.OptionSetsActive 19: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 19: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 19: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 19: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 19: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 19: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 19: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 19: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 19: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 19: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 19: [----------] 9 tests from QMMMOptionsTest (0 ms total) 19: 19: [----------] 1 test from QMMMForceProviderTest 19: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 19: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 19: [----------] 1 test from QMMMForceProviderTest (0 ms total) 19: 19: [----------] 1 test from QMMMTest 19: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 19: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 19: [----------] 1 test from QMMMTest (0 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 21 tests from 5 test suites ran. (72 ms total) 19: [ PASSED ] 21 tests. 19/87 Test #19: QMMMAppliedForcesUnitTest ................. Passed 0.13 sec test 20 Start 20: ColvarsAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests 20: Test timeout computed to be: 30 20: [==========] Running 16 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 1 test from ColvarsTest 20: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 20: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 20: [----------] 1 test from ColvarsTest (0 ms total) 20: 20: [----------] 6 tests from ColvarsOptionsTest 20: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 20: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.OptionSetsActive 20: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to 935981023 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (9 ms) 20: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 20: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 20: [----------] 6 tests from ColvarsOptionsTest (9 ms total) 20: 20: [----------] 4 tests from ColvarsPreProcessorTest 20: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -402653187 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (11 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -1217921032 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (4 ms) 20: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -18016515 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (8 ms) 20: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to 1990197101 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (11 ms) 20: [----------] 4 tests from ColvarsPreProcessorTest (35 ms total) 20: 20: [----------] 5 tests from ColvarsForceProviderTest 20: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 20: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 20: [ RUN ] ColvarsForceProviderTest.SimpleInputs 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to 1995418287 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.SimpleInputs (7 ms) 20: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -1082132234 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (7 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 21.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: NVE simulation with an initial temperature of zero: will use a Verlet 20: buffer of 10%. Check your energy drift! 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -2098177 20: 20: Generated 10 of the 10 non-bonded parameter combinations 20: 20: Generated 10 of the 10 1-4 parameter combinations 20: 20: Excluding 2 bonded neighbours molecule type 'SOL' 20: Analysing residue names: 20: There are: 4 Water residues 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForces4water (47 ms) 20: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 20: 20: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: For a correct single-point energy evaluation with nsteps = 0, use 20: continuation = yes to avoid constraining the input coordinates. 20: 20: Generating 1-4 interactions: fudge = 0.5 20: Number of degrees of freedom in T-Coupling group rest is 66.00 20: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 20: 20: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: NVE simulation: will use the initial temperature of 300.368 K for 20: determining the Verlet buffer size 20: 20: 20: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 20: You are using a plain Coulomb cut-off, which might produce artifacts. 20: You might want to consider using PME electrostatics. 20: 20: 20: 20: There were 3 NOTEs 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 20: Setting the LD random seed to -134267953 20: 20: Generated 2211 of the 2211 non-bonded parameter combinations 20: 20: Generated 2211 of the 2211 1-4 parameter combinations 20: 20: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 20: Analysing residue names: 20: There are: 2 Protein residues 20: Analysing Protein... 20: 20: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 20: 20: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 20: 20: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 20: 20: Note that mdrun will redetermine rlist based on the actual pair-list setup 20: 20: This run will generate roughly 0 Mb of data 20: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (40 ms) 20: [----------] 5 tests from ColvarsForceProviderTest (103 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 16 tests from 4 test suites ran. (149 ms total) 20: [ PASSED ] 16 tests. 20/87 Test #20: ColvarsAppliedForcesUnitTest .............. Passed 0.19 sec test 21 Start 21: AppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/applied_forces/tests 21: Test timeout computed to be: 30 21: [==========] Running 3 tests from 1 test suite. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from ElectricFieldTest 21: [ RUN ] ElectricFieldTest.Static 21: [ OK ] ElectricFieldTest.Static (0 ms) 21: [ RUN ] ElectricFieldTest.Oscillating 21: [ OK ] ElectricFieldTest.Oscillating (0 ms) 21: [ RUN ] ElectricFieldTest.Pulsed 21: [ OK ] ElectricFieldTest.Pulsed (0 ms) 21: [----------] 3 tests from ElectricFieldTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 3 tests from 1 test suite ran. (0 ms total) 21: [ PASSED ] 3 tests. 21/87 Test #21: AppliedForcesUnitTest ..................... Passed 0.03 sec test 22 Start 22: ListedForcesTest 22: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/listed_forces/tests 22: Test timeout computed to be: 30 22: [==========] Running 132 tests from 9 test suites. 22: [----------] Global test environment set-up. 22: [----------] 24 tests from Bond/ListedForcesTest 22: [ RUN ] Bond/ListedForcesTest.Ifunc/0 22: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/1 22: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/2 22: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/3 22: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/4 22: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/5 22: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/6 22: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/7 22: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/8 22: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/9 22: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/10 22: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/11 22: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/12 22: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/13 22: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/14 22: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/15 22: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/16 22: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/17 22: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/18 22: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/19 22: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/20 22: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/21 22: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/22 22: [ OK ] Bond/ListedForcesTest.Ifunc/22 (8 ms) 22: [ RUN ] Bond/ListedForcesTest.Ifunc/23 22: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 22: [----------] 24 tests from Bond/ListedForcesTest (10 ms total) 22: 22: [----------] 33 tests from Angle/ListedForcesTest 22: [ RUN ] Angle/ListedForcesTest.Ifunc/0 22: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/1 22: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/2 22: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/3 22: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/4 22: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/5 22: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/6 22: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/7 22: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/8 22: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/9 22: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/10 22: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/11 22: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/12 22: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/13 22: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/14 22: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/15 22: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/16 22: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/17 22: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/18 22: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/19 22: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/20 22: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/21 22: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/22 22: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/23 22: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/24 22: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/25 22: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/26 22: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/27 22: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/28 22: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/29 22: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/30 22: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/31 22: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 22: [ RUN ] Angle/ListedForcesTest.Ifunc/32 22: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 22: [----------] 33 tests from Angle/ListedForcesTest (2 ms total) 22: 22: [----------] 18 tests from Dihedral/ListedForcesTest 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (12 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 22: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 22: [----------] 18 tests from Dihedral/ListedForcesTest (13 ms total) 22: 22: [----------] 12 tests from Polarize/ListedForcesTest 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 22: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 22: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 22: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 22: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 22: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 22: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 22: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 22: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 22: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 22: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 22: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 22: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 22: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) 22: 22: [----------] 18 tests from Restraints/ListedForcesTest 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 22: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 22: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 22: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 22: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 22: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 22: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 22: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 22: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 22: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 22: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 22: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 22: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 22: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 22: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 22: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 22: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 22: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 22: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 22: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 22: [----------] 18 tests from Restraints/ListedForcesTest (1 ms total) 22: 22: [----------] 3 tests from BondZeroLength/ListedForcesTest 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 22: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 22: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 22: 22: [----------] 3 tests from AngleZero/ListedForcesTest 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (0 ms) 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 22: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 22: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 22: [----------] 3 tests from AngleZero/ListedForcesTest (0 ms total) 22: 22: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (12 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 22: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 22: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 22: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (13 ms total) 22: 22: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 22: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 22: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 22: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 132 tests from 9 test suites ran. (43 ms total) 22: [ PASSED ] 132 tests. 22/87 Test #22: ListedForcesTest .......................... Passed 0.11 sec test 23 Start 23: NbnxmTests 23: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/NbnxmTests.xml" 23: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/nbnxm/tests 23: Test timeout computed to be: 30 23: [==========] Running 80 tests from 3 test suites. 23: [----------] Global test environment set-up. 23: [----------] 18 tests from KernelSetupTest 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 23: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 23: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 23: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 23: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 23: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 23: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 23: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 23: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 23: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 23: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 23: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 23: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 23: [----------] 18 tests from KernelSetupTest (0 ms total) 23: 23: [----------] 60 tests from NbnxmKernelTest 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone (20 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch (12 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch (16 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom (16 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone (20 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch (16 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch (12 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom (13 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB (0 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone (12 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch (20 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch (12 ms) 23: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (13 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB (12 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone (10 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB (15 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone (19 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch (15 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch (15 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom (3 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (19 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB (18 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone (14 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch (2 ms) 23: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 23: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (10 ms) 23: [----------] 60 tests from NbnxmKernelTest (598 ms total) 23: 23: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 23: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 23: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 23: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 23: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 23: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 80 tests from 3 test suites ran. (598 ms total) 23: [ PASSED ] 80 tests. 23/87 Test #23: NbnxmTests ................................ Passed 0.68 sec test 24 Start 24: CommandLineUnitTests 24: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 24: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests 24: Test timeout computed to be: 30 24: [==========] Running 60 tests from 7 test suites. 24: [----------] Global test environment set-up. 24: [----------] 3 tests from CommandLineHelpModuleTest 24: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 24: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (0 ms) 24: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 24: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 24: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 24: [ OK ] CommandLineHelpModuleTest.ExportsHelp (13 ms) 24: [----------] 3 tests from CommandLineHelpModuleTest (14 ms total) 24: 24: [----------] 7 tests from CommandLineHelpWriterTest 24: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 24: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 24: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 24: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 24: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 24: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 24: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 24: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 24: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 24: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 24: 24: [----------] 6 tests from CommandLineModuleManagerTest 24: [ RUN ] CommandLineModuleManagerTest.RunsModule 24: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 24: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 24: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 24: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 24: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 24: 24: [----------] 13 tests from CommandLineParserTest 24: [ RUN ] CommandLineParserTest.HandlesSingleValues 24: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 24: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 24: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 24: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 24: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 24: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesString 24: [ OK ] CommandLineParserTest.HandlesString (0 ms) 24: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 24: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 24: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 24: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 24: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 24: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 24: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 24: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 24: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 24: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 24: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 24: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 24: [----------] 13 tests from CommandLineParserTest (0 ms total) 24: 24: [----------] 6 tests from CommandLineProgramContextTest 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 24: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 24: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 24: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 24: 24: [----------] 3 tests from OutputNamesTest 24: [ RUN ] OutputNamesTest.CanBeSuffixed 24: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 24: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 24: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 24: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 24: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 24: [----------] 3 tests from OutputNamesTest (0 ms total) 24: 24: [----------] 22 tests from ParseCommonArgsTest 24: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 24: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 24: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 24: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 24: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 24: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 24: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 24: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 24: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 24: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 24: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 24: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 24: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 24: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 24: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 24: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 24: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 24: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 24: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 24: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 24: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 24: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 24: Value is /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 24: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 24: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 24: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 24: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 24: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 24: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 24: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 24: [----------] 22 tests from ParseCommonArgsTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 60 tests from 7 test suites ran. (17 ms total) 24: [ PASSED ] 60 tests. 24/87 Test #24: CommandLineUnitTests ...................... Passed 0.09 sec test 25 Start 25: DomDecTests 25: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/DomDecTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests 25: Test timeout computed to be: 30 25: [==========] Running 9 tests from 2 test suites. 25: [----------] Global test environment set-up. 25: [----------] 7 tests from HashedMap 25: [ RUN ] HashedMap.InsertsFinds 25: [ OK ] HashedMap.InsertsFinds (0 ms) 25: [ RUN ] HashedMap.NegativeKeysWork 25: [ OK ] HashedMap.NegativeKeysWork (0 ms) 25: [ RUN ] HashedMap.InsertsErases 25: [ OK ] HashedMap.InsertsErases (0 ms) 25: [ RUN ] HashedMap.InsertsOrAssigns 25: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 25: [ RUN ] HashedMap.Clears 25: [ OK ] HashedMap.Clears (0 ms) 25: [ RUN ] HashedMap.LinkedEntries 25: [ OK ] HashedMap.LinkedEntries (0 ms) 25: [ RUN ] HashedMap.ResizesTable 25: [ OK ] HashedMap.ResizesTable (0 ms) 25: [----------] 7 tests from HashedMap (0 ms total) 25: 25: [----------] 2 tests from LocalAtomSetManager 25: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 25: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 25: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 25: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 25: [----------] 2 tests from LocalAtomSetManager (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 9 tests from 2 test suites ran. (0 ms total) 25: [ PASSED ] 9 tests. 25/87 Test #25: DomDecTests ............................... Passed 0.06 sec test 26 Start 26: DomDecMpiTests 26: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/domdec-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/DomDecMpiTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/domdec/tests 26: Test timeout computed to be: 30 26: [==========] Running 4 tests from 1 test suite. 26: [----------] Global test environment set-up. 26: [----------] 4 tests from HaloExchangeTest 26: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 26: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (42 ms) 26: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 26: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (51 ms) 26: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 26: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (87 ms) 26: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 26: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (91 ms) 26: [----------] 4 tests from HaloExchangeTest (274 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 4 tests from 1 test suite ran. (274 ms total) 26: [ PASSED ] 4 tests. 26/87 Test #26: DomDecMpiTests ............................ Passed 0.40 sec test 27 Start 27: EwaldUnitTests 27: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/ewald/tests 27: Test timeout computed to be: 30 27: [==========] Running 407 tests from 9 test suites. 27: [----------] Global test environment set-up. 27: [----------] 6 tests from SeparatePmeRanksPermittedTest 27: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 27: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 27: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 27: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 27: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 27: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 27: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 27: 27: [----------] 108 tests from Pme_SplineAndSpreadTest 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (67 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (4 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (13 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (12 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (12 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (22 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (12 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (12 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (7 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (17 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (9 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (10 ms) 27: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 27: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 27: [----------] 108 tests from Pme_SplineAndSpreadTest (342 ms total) 27: 27: [----------] 64 tests from Pme_SolveTest 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (12 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (16 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (16 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [----------] 64 tests from Pme_SolveTest (54 ms total) 27: 27: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (12 ms) 27: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (15 ms total) 27: 27: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (16 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 27: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 27: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (21 ms total) 27: 27: [----------] 64 tests from PmeDiffEps_SolveTest 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (16 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (16 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 27: Test is being skipped because: 27: CPU PME solve does not implement XYZ grid ordering 27: 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 27: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 27: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 27: [----------] 64 tests from PmeDiffEps_SolveTest (41 ms total) 27: 27: [----------] 72 tests from Pme_GatherTest 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (12 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (16 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (16 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 27: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 27: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 27: [----------] 72 tests from Pme_GatherTest (54 ms total) 27: 27: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 27: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 27: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 27: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 27: 27: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (18 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (21 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (16 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (13 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (16 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (17 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (18 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (12 ms) 27: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 27: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 27: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (155 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 407 tests from 9 test suites ran. (686 ms total) 27: [ PASSED ] 311 tests. 27: [ SKIPPED ] 96 tests, listed below: 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 27: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 27/87 Test #27: EwaldUnitTests ............................ Passed 0.83 sec test 28 Start 28: FFTUnitTests 28: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fft/tests 28: Test timeout computed to be: 1920 28: [==========] Running 15 tests from 4 test suites. 28: [----------] Global test environment set-up. 28: [----------] 2 tests from ManyFFTTest 28: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 28: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (7 ms) 28: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 28: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (8 ms) 28: [----------] 2 tests from ManyFFTTest (17 ms total) 28: 28: [----------] 1 test from FFTTest 28: [ RUN ] FFTTest.Real2DLength18_15Test 28: [ OK ] FFTTest.Real2DLength18_15Test (9 ms) 28: [----------] 1 test from FFTTest (9 ms total) 28: 28: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 28: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (17 ms) 28: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 28: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (2 ms) 28: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (22 ms total) 28: 28: [----------] 2 tests from Works/ParameterizedFFTTest3D 28: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 28: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 28: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 28: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (4 ms) 28: [----------] 2 tests from Works/ParameterizedFFTTest3D (5 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 15 tests from 4 test suites ran. (54 ms total) 28: [ PASSED ] 15 tests. 28/87 Test #28: FFTUnitTests .............................. Passed 0.14 sec test 29 Start 29: GpuUtilsUnitTests 29: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gpu_utils/tests 29: Test timeout computed to be: 30 29: [==========] Running 64 tests from 22 test suites. 29: [----------] Global test environment set-up. 29: [----------] 2 tests from ClfftInitializer 29: [ RUN ] ClfftInitializer.SingleInitializationWorks 29: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 29: [ RUN ] ClfftInitializer.TwoInitializationsWork 29: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 29: [----------] 2 tests from ClfftInitializer (0 ms total) 29: 29: [----------] 1 test from DevicesAvailable 29: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 29: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 29: [----------] 1 test from DevicesAvailable (0 ms total) 29: 29: [----------] 1 test from DeviceStreamManagerTest 29: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 29: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 29: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 29: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 29: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 29: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 29: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 29: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 29: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 29: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 29: 29: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 29: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 29: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 29: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 29: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 29: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 29: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.Swap 29: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/0.Comparison 29: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 29: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 29: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.Swap 29: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/1.Comparison 29: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 29: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.Swap 29: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/2.Comparison 29: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 29: 29: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 29: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 29: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 29: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 29: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.Swap 29: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 29: [ RUN ] HostAllocatorTestNoMem/3.Comparison 29: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 29: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 29: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 29: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 29: 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 29: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 29: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 29: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 29: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 29: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 29: 29: [----------] 1 test from HostAllocatorUntypedTest 29: [ RUN ] HostAllocatorUntypedTest.Comparison 29: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 29: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/0.Move 29: [ OK ] AllocatorTest/0.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/0 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/1.Move 29: [ OK ] AllocatorTest/1.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/1 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 29: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/2.Move 29: [ OK ] AllocatorTest/2.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/2 (0 ms total) 29: 29: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 29: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 29: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 29: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 29: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 29: [ RUN ] AllocatorTest/3.Move 29: [ OK ] AllocatorTest/3.Move (0 ms) 29: [----------] 4 tests from AllocatorTest/3 (0 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 64 tests from 22 test suites ran. (0 ms total) 29: [ PASSED ] 64 tests. 29/87 Test #29: GpuUtilsUnitTests ......................... Passed 0.10 sec test 30 Start 30: HardwareUnitTests 30: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/hardware/tests 30: Test timeout computed to be: 30 30: [==========] Running 21 tests from 9 test suites. 30: [----------] Global test environment set-up. 30: [----------] 1 test from CpuInfoTest 30: [ RUN ] CpuInfoTest.SupportLevel 30: [ OK ] CpuInfoTest.SupportLevel (0 ms) 30: [----------] 1 test from CpuInfoTest (0 ms total) 30: 30: [----------] 4 tests from HardwareTopologyTest 30: [ RUN ] HardwareTopologyTest.Execute 30: [ OK ] HardwareTopologyTest.Execute (37 ms) 30: [ RUN ] HardwareTopologyTest.HwlocExecute 30: [ OK ] HardwareTopologyTest.HwlocExecute (23 ms) 30: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 30: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (36 ms) 30: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 30: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (23 ms) 30: [----------] 4 tests from HardwareTopologyTest (132 ms total) 30: 30: [----------] 1 test from DevicesManagerTest 30: [ RUN ] DevicesManagerTest.Serialization 30: [ OK ] DevicesManagerTest.Serialization (0 ms) 30: [----------] 1 test from DevicesManagerTest (0 ms total) 30: 30: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (12 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 30: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 30: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 30: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (14 ms total) 30: 30: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (10 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 30: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 30: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 30: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (12 ms total) 30: 30: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 30: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 30: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (17 ms) 30: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 30: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (8 ms) 30: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (26 ms total) 30: 30: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 30: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (59 ms) 30: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (59 ms total) 30: 30: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 30: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (51 ms) 30: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (51 ms total) 30: 30: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 30: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 30: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (136 ms) 30: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (136 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 21 tests from 9 test suites ran. (433 ms total) 30: [ PASSED ] 21 tests. 30/87 Test #30: HardwareUnitTests ......................... Passed 0.50 sec test 31 Start 31: MathUnitTests 31: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/math/tests 31: Test timeout computed to be: 30 31: [==========] Running 304 tests from 38 test suites. 31: [----------] Global test environment set-up. 31: [----------] 1 test from EmptyArrayRefWithPaddingTest 31: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 31: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 31: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 31: 31: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 31: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 31: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 31: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 31: 31: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 31: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 31: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 31: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 31: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 31: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 31: 31: [----------] 2 tests from InvertBoxMatrixTest 31: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 31: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 31: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 31: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 31: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 31: 31: [----------] 11 tests from TranslateAndScaleTest 31: [ RUN ] TranslateAndScaleTest.identityTransformation 31: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 31: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 31: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 31: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 31: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 31: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingIdentity 31: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 31: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 31: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 31: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 31: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 31: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 31: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 31: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 31: 31: [----------] 3 tests from AffineTransformationTest 31: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 31: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 31: [ RUN ] AffineTransformationTest.applyTransformationToVectors 31: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 31: [ RUN ] AffineTransformationTest.retrieveGradient 31: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 31: [----------] 3 tests from AffineTransformationTest (0 ms total) 31: 31: [----------] 14 tests from DensitySimilarityTest 31: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 31: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 31: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 31: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 31: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 31: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 31: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 31: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 31: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 31: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 31: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 31: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (55 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 31: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (59 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 31: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (0 ms) 31: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 31: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.NormalizationCorrect 31: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 31: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 31: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 31: [----------] 14 tests from DensitySimilarityTest (117 ms total) 31: 31: [----------] 6 tests from StructureSimilarityTest 31: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 31: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 31: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 31: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 31: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 31: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 31: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 31: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 31: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 31: [----------] 6 tests from StructureSimilarityTest (0 ms total) 31: 31: [----------] 8 tests from ExponentialMovingAverage 31: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 31: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 31: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 31: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 31: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 31: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 31: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 31: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 31: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 31: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 31: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 31: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 31: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 31: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 31: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 31: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 31: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 31: 31: [----------] 21 tests from FunctionTest 31: [ RUN ] FunctionTest.StaticLog2 31: [ OK ] FunctionTest.StaticLog2 (0 ms) 31: [ RUN ] FunctionTest.Log2I32Bit 31: [ OK ] FunctionTest.Log2I32Bit (0 ms) 31: [ RUN ] FunctionTest.Log2I64Bit 31: [ OK ] FunctionTest.Log2I64Bit (0 ms) 31: [ RUN ] FunctionTest.GreatestCommonDivisor 31: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 31: [ RUN ] FunctionTest.InvsqrtFloat 31: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 31: [ RUN ] FunctionTest.InvsqrtDouble 31: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 31: [ RUN ] FunctionTest.InvsqrtInteger 31: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 31: [ RUN ] FunctionTest.InvcbrtFloat 31: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 31: [ RUN ] FunctionTest.InvcbrtDouble 31: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 31: [ RUN ] FunctionTest.InvcbrtInteger 31: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 31: [ RUN ] FunctionTest.SixthrootFloat 31: [ OK ] FunctionTest.SixthrootFloat (0 ms) 31: [ RUN ] FunctionTest.SixthrootDouble 31: [ OK ] FunctionTest.SixthrootDouble (0 ms) 31: [ RUN ] FunctionTest.SixthrootInteger 31: [ OK ] FunctionTest.SixthrootInteger (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootFloat 31: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootDouble 31: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 31: [ RUN ] FunctionTest.InvsixthrootInteger 31: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 31: [ RUN ] FunctionTest.Powers 31: [ OK ] FunctionTest.Powers (0 ms) 31: [ RUN ] FunctionTest.ErfInvFloat 31: [ OK ] FunctionTest.ErfInvFloat (0 ms) 31: [ RUN ] FunctionTest.ErfInvDouble 31: [ OK ] FunctionTest.ErfInvDouble (0 ms) 31: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 31: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 31: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 31: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 31: [----------] 21 tests from FunctionTest (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 31: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 31: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 31: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 31: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 31: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 31: 31: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 31: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 31: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 31: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 31: 31: [----------] 4 tests from GaussianOn1DLattice 31: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 31: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 31: [ RUN ] GaussianOn1DLattice.isCorrect 31: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 31: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 31: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 31: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 31: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 31: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 31: 31: [----------] 9 tests from GaussTransformTest 31: [ RUN ] GaussTransformTest.isZeroUponConstruction 31: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 31: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 31: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 31: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 31: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 31: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 31: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 31: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 31: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 31: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 31: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 31: [ RUN ] GaussTransformTest.view 31: [ OK ] GaussTransformTest.view (0 ms) 31: [----------] 9 tests from GaussTransformTest (0 ms total) 31: 31: [----------] 3 tests from DensityFittingForce 31: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 31: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 31: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 31: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 31: [ RUN ] DensityFittingForce.pullsTowardsDerivative 31: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 31: [----------] 3 tests from DensityFittingForce (0 ms total) 31: 31: [----------] 2 tests from InvertMatrixTest 31: [ RUN ] InvertMatrixTest.IdentityIsImpotent 31: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 31: [ RUN ] InvertMatrixTest.ComputesInverse 31: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 31: [----------] 2 tests from InvertMatrixTest (0 ms total) 31: 31: [----------] 17 tests from MatrixTest 31: [ RUN ] MatrixTest.canSetFromArray 31: [ OK ] MatrixTest.canSetFromArray (0 ms) 31: [ RUN ] MatrixTest.canSetStaticallyFromList 31: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 31: [ RUN ] MatrixTest.canConstructAndFill 31: [ OK ] MatrixTest.canConstructAndFill (0 ms) 31: [ RUN ] MatrixTest.canSetValues 31: [ OK ] MatrixTest.canSetValues (0 ms) 31: [ RUN ] MatrixTest.canCopyAssign 31: [ OK ] MatrixTest.canCopyAssign (0 ms) 31: [ RUN ] MatrixTest.canSwap 31: [ OK ] MatrixTest.canSwap (0 ms) 31: [ RUN ] MatrixTest.staticMultiDimArrayExtent 31: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 31: [ RUN ] MatrixTest.determinantWorks 31: [ OK ] MatrixTest.determinantWorks (0 ms) 31: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 31: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 31: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 31: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 31: [ RUN ] MatrixTest.traceWorks 31: [ OK ] MatrixTest.traceWorks (0 ms) 31: [ RUN ] MatrixTest.transposeWorks 31: [ OK ] MatrixTest.transposeWorks (0 ms) 31: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 31: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 31: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 31: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 31: [ RUN ] MatrixTest.canFillLegacyMatrix 31: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 31: [ RUN ] MatrixTest.IdentityMatrix 31: [ OK ] MatrixTest.IdentityMatrix (0 ms) 31: [ RUN ] MatrixTest.MatrixVectorMultiplication 31: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 31: [----------] 17 tests from MatrixTest (0 ms total) 31: 31: [----------] 25 tests from MultiDimArrayTest 31: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 31: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 31: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 31: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 31: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 31: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 31: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 31: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 31: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 31: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 31: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 31: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 31: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSwapStatic 31: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 31: [ RUN ] MultiDimArrayTest.canSwapDynamic 31: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 31: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 31: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 31: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 31: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 31: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 31: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 31: [ RUN ] MultiDimArrayTest.conversionToView 31: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 31: [ RUN ] MultiDimArrayTest.conversionToConstView 31: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 31: [ RUN ] MultiDimArrayTest.viewBegin 31: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 31: [ RUN ] MultiDimArrayTest.viewEnd 31: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 31: [ RUN ] MultiDimArrayTest.constViewConstBegin 31: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 31: [ RUN ] MultiDimArrayTest.constViewConstEnd 31: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 31: [----------] 25 tests from MultiDimArrayTest (0 ms total) 31: 31: [----------] 4 tests from MultiDimArrayToMdSpanTest 31: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 31: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 31: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 31: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 31: 31: [----------] 9 tests from NelderMeadSimplexTest 31: [ RUN ] NelderMeadSimplexTest.BestVertex 31: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 31: [ RUN ] NelderMeadSimplexTest.WorstVertex 31: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 31: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 31: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 31: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 31: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 31: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 31: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 31: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 31: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 31: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 31: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 31: [ RUN ] NelderMeadSimplexTest.OrientedLength 31: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 31: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 31: 31: [----------] 2 tests from NelderMead 31: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 31: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (0 ms) 31: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 31: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 31: [----------] 2 tests from NelderMead (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ResizeWorks 31: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ReserveWorks 31: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanCopyAssign 31: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanMoveAssign 31: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/0.CanSwap 31: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ResizeWorks 31: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ReserveWorks 31: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanCopyAssign 31: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanMoveAssign 31: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/1.CanSwap 31: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 31: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ResizeWorks 31: [ OK ] PaddedVectorTest/2.ResizeWorks (16 ms) 31: [ RUN ] PaddedVectorTest/2.ReserveWorks 31: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanCopyAssign 31: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanMoveAssign 31: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/2.CanSwap 31: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/2 (16 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 31: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ResizeWorks 31: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ReserveWorks 31: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanCopyAssign 31: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanMoveAssign 31: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/3.CanSwap 31: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 31: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ResizeWorks 31: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ReserveWorks 31: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanCopyAssign 31: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanMoveAssign 31: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/4.CanSwap 31: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ResizeWorks 31: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ReserveWorks 31: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanCopyAssign 31: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanMoveAssign 31: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/5.CanSwap 31: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ResizeWorks 31: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ReserveWorks 31: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanCopyAssign 31: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanMoveAssign 31: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/6.CanSwap 31: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 31: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ResizeWorks 31: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ReserveWorks 31: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanCopyAssign 31: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanMoveAssign 31: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/7.CanSwap 31: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 31: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ResizeWorks 31: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ReserveWorks 31: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanCopyAssign 31: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanMoveAssign 31: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/8.CanSwap 31: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 31: 31: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 31: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 31: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ResizeWorks 31: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ReserveWorks 31: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 31: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 31: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 31: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 31: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 31: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 31: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanCopyAssign 31: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanMoveAssign 31: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 31: [ RUN ] PaddedVectorTest/9.CanSwap 31: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 31: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 31: 31: [----------] 40 tests from RVecTest 31: [ RUN ] RVecTest.CanBeStoredInVector 31: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 31: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 31: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 31: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 31: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 31: [ RUN ] RVecTest.WorksAsMutable_rvec 31: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 31: [ RUN ] RVecTest.WorksAs_rvec_Array 31: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 31: [ RUN ] RVecTest.ComparesEqual 31: [ OK ] RVecTest.ComparesEqual (0 ms) 31: [ RUN ] RVecTest.ComparesUnequal 31: [ OK ] RVecTest.ComparesUnequal (0 ms) 31: [ RUN ] RVecTest.CanAddRVecToRvec 31: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 31: [ RUN ] RVecTest.CanAddAssignRVecToRvec 31: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 31: [ RUN ] RVecTest.CanSubtractRVecFromRvec 31: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 31: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 31: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 31: [ RUN ] RVecTest.CanDotProductRVecByRvec 31: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 31: [ RUN ] RVecTest.CanCrossProductRVecByRvec 31: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 31: [ RUN ] RVecTest.CanDivideRVecInplace 31: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 31: [ RUN ] RVecTest.CanScaleRVec 31: [ OK ] RVecTest.CanScaleRVec (0 ms) 31: [ RUN ] RVecTest.CanDivideRVec 31: [ OK ] RVecTest.CanDivideRVec (0 ms) 31: [ RUN ] RVecTest.CanDoUnitvFromRVec 31: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 31: [ RUN ] RVecTest.CanSqLengthOfRVec 31: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanLengthOfRVec 31: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanCastToRVec 31: [ OK ] RVecTest.CanCastToRVec (0 ms) 31: [ RUN ] RVecTest.CanCastToDVec 31: [ OK ] RVecTest.CanCastToDVec (0 ms) 31: [ RUN ] RVecTest.CanLeftScalarMultiply 31: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 31: [ RUN ] RVecTest.CanRightScalarMultiply 31: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 31: [ RUN ] RVecTest.CanGetUnitvFromRVec 31: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 31: [ RUN ] RVecTest.CanGetSqLengthOfRVec 31: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanGetLengthOfRVec 31: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 31: [ RUN ] RVecTest.CanDoCrossProductOfRVec 31: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 31: [ RUN ] RVecTest.CanDoDotProductOfRVec 31: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 31: [ RUN ] RVecTest.CanScaleByVector 31: [ OK ] RVecTest.CanScaleByVector (0 ms) 31: [ RUN ] RVecTest.CanNegate 31: [ OK ] RVecTest.CanNegate (0 ms) 31: [ RUN ] RVecTest.asIVec 31: [ OK ] RVecTest.asIVec (0 ms) 31: [ RUN ] RVecTest.elementWiseMin 31: [ OK ] RVecTest.elementWiseMin (0 ms) 31: [ RUN ] RVecTest.elementWiseMax 31: [ OK ] RVecTest.elementWiseMax (0 ms) 31: [ RUN ] RVecTest.WorksAs_dvec_Reference 31: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 31: [ RUN ] RVecTest.WorksAs_ivec_Reference 31: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 31: [ RUN ] RVecTest.WorksAs_rvec_Reference 31: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 31: [ RUN ] RVecTest.CopyConstructorWorks 31: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 31: [ RUN ] RVecTest.CopyAssignmentWorks 31: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 31: [ RUN ] RVecTest.MoveConstructorWorks 31: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 31: [ RUN ] RVecTest.MoveAssignmentWorks 31: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 31: [----------] 40 tests from RVecTest (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 304 tests from 38 test suites ran. (135 ms total) 31: [ PASSED ] 304 tests. 31/87 Test #31: MathUnitTests ............................. Passed 0.23 sec test 32 Start 32: MdrunUtilityUnitTests 32: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests 32: Test timeout computed to be: 30 32: [==========] Running 21 tests from 2 test suites. 32: [----------] Global test environment set-up. 32: [----------] 4 tests from MDModulesNotifierTest 32: [ RUN ] MDModulesNotifierTest.AddConsumer 32: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 32: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 32: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 32: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 32: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 32: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 32: 32: [----------] 17 tests from ThreadAffinityTest 32: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 32: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 32: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 32: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 32: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 32: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 32: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 32: NOTE: Affinity setting failed. 32: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 32: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (12 ms) 32: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 32: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 32: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 32: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (7 ms) 32: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 32: NOTE: Affinity setting for 1/2 threads failed. 32: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (4 ms) 32: [----------] 17 tests from ThreadAffinityTest (25 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 21 tests from 2 test suites ran. (25 ms total) 32: [ PASSED ] 21 tests. 32/87 Test #32: MdrunUtilityUnitTests ..................... Passed 0.09 sec test 33 Start 33: MdrunUtilityMpiUnitTests 33: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdrunutility/tests 33: Test timeout computed to be: 30 33: [==========] Running 13 tests from 2 test suites. 33: [----------] Global test environment set-up. 33: [----------] 6 tests from ThreadAffinityMultiRankTest 33: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 33: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (246 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 33: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (347 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 33: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (196 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 33: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (79 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 33: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (251 ms) 33: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 33: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (211 ms) 33: [----------] 6 tests from ThreadAffinityMultiRankTest (1334 ms total) 33: 33: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (184 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (179 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (212 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (207 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (219 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (164 ms) 33: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 33: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (211 ms) 33: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (1379 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 13 tests from 2 test suites ran. (2714 ms total) 33: [ PASSED ] 13 tests. 33/87 Test #33: MdrunUtilityMpiUnitTests .................. Passed 2.76 sec test 34 Start 34: MDSpanTests 34: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MDSpanTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdspan/tests 34: Test timeout computed to be: 30 34: [==========] Running 32 tests from 7 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from BasicAccessorPolicy 34: [ RUN ] BasicAccessorPolicy.Decay 34: [ OK ] BasicAccessorPolicy.Decay (0 ms) 34: [ RUN ] BasicAccessorPolicy.Access 34: [ OK ] BasicAccessorPolicy.Access (0 ms) 34: [ RUN ] BasicAccessorPolicy.Offset 34: [ OK ] BasicAccessorPolicy.Offset (0 ms) 34: [ RUN ] BasicAccessorPolicy.CopyAccessor 34: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 34: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 34: 34: [----------] 4 tests from ExtentsTest 34: [ RUN ] ExtentsTest.Construction 34: [ OK ] ExtentsTest.Construction (0 ms) 34: [ RUN ] ExtentsTest.PurelyStatic 34: [ OK ] ExtentsTest.PurelyStatic (0 ms) 34: [ RUN ] ExtentsTest.RankNought 34: [ OK ] ExtentsTest.RankNought (0 ms) 34: [ RUN ] ExtentsTest.Assignment 34: [ OK ] ExtentsTest.Assignment (0 ms) 34: [----------] 4 tests from ExtentsTest (0 ms total) 34: 34: [----------] 8 tests from MdSpanExtension 34: [ RUN ] MdSpanExtension.SlicingAllStatic 34: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 34: [ RUN ] MdSpanExtension.SlicingDynamic 34: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 34: [ RUN ] MdSpanExtension.SlicingAllStatic3D 34: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 34: [ RUN ] MdSpanExtension.SlicingEqualsView3D 34: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 34: [ RUN ] MdSpanExtension.additionWorks 34: [ OK ] MdSpanExtension.additionWorks (0 ms) 34: [ RUN ] MdSpanExtension.subtractionWorks 34: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 34: [ RUN ] MdSpanExtension.multiplicationWorks 34: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 34: [ RUN ] MdSpanExtension.divisionWorks 34: [ OK ] MdSpanExtension.divisionWorks (0 ms) 34: [----------] 8 tests from MdSpanExtension (0 ms total) 34: 34: [----------] 3 tests from LayoutTests 34: [ RUN ] LayoutTests.LayoutRightConstruction 34: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 34: [ RUN ] LayoutTests.LayoutRightProperties 34: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 34: [ RUN ] LayoutTests.LayoutRightOperator 34: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 34: [----------] 3 tests from LayoutTests (0 ms total) 34: 34: [----------] 1 test from MdSpanTest 34: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 34: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 34: [----------] 1 test from MdSpanTest (0 ms total) 34: 34: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 34: [ RUN ] MdSpanTest/0.Rank 34: [ OK ] MdSpanTest/0.Rank (0 ms) 34: [ RUN ] MdSpanTest/0.DynamicRank 34: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 34: [ RUN ] MdSpanTest/0.Extents 34: [ OK ] MdSpanTest/0.Extents (0 ms) 34: [ RUN ] MdSpanTest/0.Strides 34: [ OK ] MdSpanTest/0.Strides (0 ms) 34: [ RUN ] MdSpanTest/0.Properties 34: [ OK ] MdSpanTest/0.Properties (0 ms) 34: [ RUN ] MdSpanTest/0.Operator 34: [ OK ] MdSpanTest/0.Operator (0 ms) 34: [----------] 6 tests from MdSpanTest/0 (0 ms total) 34: 34: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 34: [ RUN ] MdSpanTest/1.Rank 34: [ OK ] MdSpanTest/1.Rank (0 ms) 34: [ RUN ] MdSpanTest/1.DynamicRank 34: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 34: [ RUN ] MdSpanTest/1.Extents 34: [ OK ] MdSpanTest/1.Extents (0 ms) 34: [ RUN ] MdSpanTest/1.Strides 34: [ OK ] MdSpanTest/1.Strides (0 ms) 34: [ RUN ] MdSpanTest/1.Properties 34: [ OK ] MdSpanTest/1.Properties (0 ms) 34: [ RUN ] MdSpanTest/1.Operator 34: [ OK ] MdSpanTest/1.Operator (0 ms) 34: [----------] 6 tests from MdSpanTest/1 (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 32 tests from 7 test suites ran. (12 ms total) 34: [ PASSED ] 32 tests. 34/87 Test #34: MDSpanTests ............................... Passed 0.06 sec test 35 Start 35: MdtypesUnitTest 35: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdtypesUnitTest.xml" 35: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/mdtypes/tests 35: Test timeout computed to be: 30 35: [==========] Running 97 tests from 7 test suites. 35: [----------] Global test environment set-up. 35: [----------] 4 tests from ForeingLambdaTermsDhdl 35: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 35: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 35: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 35: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 35: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 35: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 35: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 35: 35: [----------] 4 tests from ObservablesReducerTest 35: [ RUN ] ObservablesReducerTest.CanMoveAssign 35: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 35: [ RUN ] ObservablesReducerTest.CanMoveConstruct 35: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 35: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 35: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 35: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 35: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 35: [----------] 4 tests from ObservablesReducerTest (0 ms total) 35: 35: [----------] 2 tests from CheckpointDataTest 35: [ RUN ] CheckpointDataTest.SingleDataTest 35: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 35: [ RUN ] CheckpointDataTest.MultiDataTest 35: [ OK ] CheckpointDataTest.MultiDataTest (2 ms) 35: [----------] 2 tests from CheckpointDataTest (2 ms total) 35: 35: [----------] 7 tests from ForceBuffers 35: [ RUN ] ForceBuffers.ConstructsUnpinned 35: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 35: [ RUN ] ForceBuffers.ConstructsPinned 35: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 35: [ RUN ] ForceBuffers.ConstructsEmpty 35: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 35: [ RUN ] ForceBuffers.ResizeWorks 35: [ OK ] ForceBuffers.ResizeWorks (0 ms) 35: [ RUN ] ForceBuffers.PaddingWorks 35: [ OK ] ForceBuffers.PaddingWorks (0 ms) 35: [ RUN ] ForceBuffers.CopyWorks 35: [ OK ] ForceBuffers.CopyWorks (0 ms) 35: [ RUN ] ForceBuffers.CopyDoesNotPin 35: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 35: [----------] 7 tests from ForceBuffers (0 ms total) 35: 35: [----------] 5 tests from MultipleTimeStepping 35: [ RUN ] MultipleTimeStepping.ChecksNumLevels 35: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 35: [ RUN ] MultipleTimeStepping.SelectsForceGroups 35: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksStepFactor 35: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 35: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (0 ms) 35: [ RUN ] MultipleTimeStepping.ChecksIntegrator 35: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 35: [----------] 5 tests from MultipleTimeStepping (0 ms total) 35: 35: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 35: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 35: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 35: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 35: 35: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 35: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 35: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 35: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 97 tests from 7 test suites ran. (19 ms total) 35: [ PASSED ] 97 tests. 35/87 Test #35: MdtypesUnitTest ........................... Passed 0.10 sec test 36 Start 36: OnlineHelpUnitTests 36: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/onlinehelp/tests 36: Test timeout computed to be: 30 36: [==========] Running 22 tests from 4 test suites. 36: [----------] Global test environment set-up. 36: [----------] 6 tests from TextTableFormatterTest 36: [ RUN ] TextTableFormatterTest.HandlesBasicCase 36: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 36: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesIndentation 36: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 36: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 36: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 36: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 36: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (12 ms) 36: [----------] 6 tests from TextTableFormatterTest (12 ms total) 36: 36: [----------] 3 tests from HelpManagerTest 36: [ RUN ] HelpManagerTest.HandlesRootTopic 36: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 36: [ RUN ] HelpManagerTest.HandlesSubTopics 36: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 36: [ RUN ] HelpManagerTest.HandlesInvalidTopics 36: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 36: [----------] 3 tests from HelpManagerTest (0 ms total) 36: 36: [----------] 2 tests from HelpTopicFormattingTest 36: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 36: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 36: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 36: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 36: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 36: 36: [----------] 11 tests from HelpWriterContextTest 36: [ RUN ] HelpWriterContextTest.FormatsParagraphs 36: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 36: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 36: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 36: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralText 36: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 36: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 36: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsBulletList 36: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 36: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 36: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsGridTable 36: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 36: [ RUN ] HelpWriterContextTest.FormatsTitles 36: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 36: [----------] 11 tests from HelpWriterContextTest (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 22 tests from 4 test suites ran. (13 ms total) 36: [ PASSED ] 22 tests. 36/87 Test #36: OnlineHelpUnitTests ....................... Passed 0.08 sec test 37 Start 37: OptionsUnitTests 37: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 37: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/tests 37: Test timeout computed to be: 30 37: [==========] Running 111 tests from 18 test suites. 37: [----------] Global test environment set-up. 37: [----------] 5 tests from AbstractOptionStorageTest 37: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 37: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 37: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 37: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 37: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 37: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (16 ms) 37: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 37: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 37: [----------] 5 tests from AbstractOptionStorageTest (16 ms total) 37: 37: [----------] 10 tests from FileNameOptionTest 37: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 37: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 37: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 37: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 37: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 37: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 37: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 37: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 37: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 37: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 37: [----------] 10 tests from FileNameOptionTest (0 ms total) 37: 37: [----------] 15 tests from FileNameOptionManagerTest 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 37: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 37: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 37: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 37: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 37: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 37: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 37: [----------] 15 tests from FileNameOptionManagerTest (0 ms total) 37: 37: [----------] 1 test from OptionsTest 37: [ RUN ] OptionsTest.FailsOnNonsafeStorage 37: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 37: [----------] 1 test from OptionsTest (0 ms total) 37: 37: [----------] 9 tests from OptionsAssignerTest 37: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 37: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 37: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 37: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 37: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMissingValue 37: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesExtraValue 37: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesGroups 37: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesSections 37: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 37: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 37: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 37: [----------] 9 tests from OptionsAssignerTest (0 ms total) 37: 37: [----------] 4 tests from OptionsAssignerBooleanTest 37: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 37: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 37: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 37: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 37: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 37: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 37: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 37: 37: [----------] 13 tests from OptionsAssignerIntegerTest 37: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 37: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 37: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 37: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 37: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 37: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 37: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 37: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 37: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 37: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 37: 37: [----------] 5 tests from OptionsAssignerDoubleTest 37: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 37: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 37: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 37: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 37: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 37: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 37: 37: [----------] 9 tests from OptionsAssignerStringTest 37: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 37: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 37: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 37: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 37: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 37: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 37: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 37: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 37: 37: [----------] 6 tests from OptionsAssignerEnumTest 37: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 37: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 37: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 37: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 37: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 37: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 37: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 37: 37: [----------] 8 tests from RepeatingOptionSectionTest 37: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 37: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 37: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 37: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 37: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 37: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 37: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 37: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 37: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 37: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 37: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 37: 37: [----------] 1 test from TimeUnitManagerTest 37: [ RUN ] TimeUnitManagerTest.BasicOperations 37: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 37: [----------] 1 test from TimeUnitManagerTest (0 ms total) 37: 37: [----------] 4 tests from TimeUnitBehaviorTest 37: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 37: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 37: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 37: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 37: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 37: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 37: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 37: 37: [----------] 2 tests from TreeValueSupportAssignTest 37: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 37: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 37: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 37: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 37: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 37: 37: [----------] 1 test from TreeValueSupportAssignErrorTest 37: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 37: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 37: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 37: 37: [----------] 5 tests from TreeValueSupportCheckTest 37: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 37: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 37: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 37: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 37: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 37: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 37: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 37: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 37: 37: [----------] 6 tests from TreeValueSupportAdjustTest 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 37: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 37: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 37: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 37: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 37: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 37: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 37: 37: [----------] 7 tests from TreeValueSupportTest 37: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 37: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 37: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsInt64Option 37: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsStringOption 37: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsFloatOption 37: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 37: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 37: [ RUN ] TreeValueSupportTest.SupportsEnumOption 37: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 37: [----------] 7 tests from TreeValueSupportTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 111 tests from 18 test suites ran. (18 ms total) 37: [ PASSED ] 111 tests. 37/87 Test #37: OptionsUnitTests .......................... Passed 0.11 sec test 38 Start 38: PbcutilUnitTest 38: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml" 38: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pbcutil/tests 38: Test timeout computed to be: 30 38: [==========] Running 37 tests from 5 test suites. 38: [----------] Global test environment set-up. 38: [----------] 1 test from ShiftTest 38: [ RUN ] ShiftTest.CoordinateShiftWorks 38: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 38: [----------] 1 test from ShiftTest (0 ms total) 38: 38: [----------] 2 tests from MShift 38: [ RUN ] MShift.shiftsAndUnshifts 38: [ OK ] MShift.shiftsAndUnshifts (0 ms) 38: [ RUN ] MShift.shiftsAndUnshiftsSelf 38: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 38: [----------] 2 tests from MShift (0 ms total) 38: 38: [----------] 5 tests from PbcTest 38: [ RUN ] PbcTest.CalcShiftsWorks 38: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 38: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 38: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 38: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 38: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 38: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 38: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 38: [----------] 5 tests from PbcTest (0 ms total) 38: 38: [----------] 2 tests from PbcEnumsTest 38: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 38: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 38: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 38: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 38: [----------] 2 tests from PbcEnumsTest (0 ms total) 38: 38: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (12 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 38: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 38: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 38: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (14 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 37 tests from 5 test suites ran. (15 ms total) 38: [ PASSED ] 37 tests. 38/87 Test #38: PbcutilUnitTest ........................... Passed 0.08 sec test 39 Start 39: RandomUnitTests 39: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/random/tests 39: Test timeout computed to be: 30 39: [==========] Running 44 tests from 10 test suites. 39: [----------] Global test environment set-up. 39: [----------] 4 tests from ExponentialDistributionTest 39: [ RUN ] ExponentialDistributionTest.Output 39: [ OK ] ExponentialDistributionTest.Output (0 ms) 39: [ RUN ] ExponentialDistributionTest.Logical 39: [ OK ] ExponentialDistributionTest.Logical (0 ms) 39: [ RUN ] ExponentialDistributionTest.Reset 39: [ OK ] ExponentialDistributionTest.Reset (0 ms) 39: [ RUN ] ExponentialDistributionTest.AltParam 39: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 39: 39: [----------] 4 tests from GammaDistributionTest 39: [ RUN ] GammaDistributionTest.Output 39: [ OK ] GammaDistributionTest.Output (0 ms) 39: [ RUN ] GammaDistributionTest.Logical 39: [ OK ] GammaDistributionTest.Logical (0 ms) 39: [ RUN ] GammaDistributionTest.Reset 39: [ OK ] GammaDistributionTest.Reset (0 ms) 39: [ RUN ] GammaDistributionTest.AltParam 39: [ OK ] GammaDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from GammaDistributionTest (0 ms total) 39: 39: [----------] 4 tests from NormalDistributionTest 39: [ RUN ] NormalDistributionTest.Output 39: [ OK ] NormalDistributionTest.Output (0 ms) 39: [ RUN ] NormalDistributionTest.Logical 39: [ OK ] NormalDistributionTest.Logical (0 ms) 39: [ RUN ] NormalDistributionTest.Reset 39: [ OK ] NormalDistributionTest.Reset (0 ms) 39: [ RUN ] NormalDistributionTest.AltParam 39: [ OK ] NormalDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from NormalDistributionTest (0 ms total) 39: 39: [----------] 1 test from SeedTest 39: [ RUN ] SeedTest.makeRandomSeed 39: [ OK ] SeedTest.makeRandomSeed (0 ms) 39: [----------] 1 test from SeedTest (0 ms total) 39: 39: [----------] 6 tests from TabulatedNormalDistributionTest 39: [ RUN ] TabulatedNormalDistributionTest.Output14 39: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Output16 39: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 39: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Logical 39: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.Reset 39: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 39: [ RUN ] TabulatedNormalDistributionTest.AltParam 39: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 39: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 39: 39: [----------] 1 test from TabulatedNormalDistributionTableTest 39: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 39: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 39: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 39: 39: [----------] 6 tests from ThreeFry2x64Test 39: [ RUN ] ThreeFry2x64Test.Logical 39: [ OK ] ThreeFry2x64Test.Logical (0 ms) 39: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 39: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 39: [ RUN ] ThreeFry2x64Test.Reseed 39: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 39: [ RUN ] ThreeFry2x64Test.Discard 39: [ OK ] ThreeFry2x64Test.Discard (0 ms) 39: [ RUN ] ThreeFry2x64Test.InvalidCounter 39: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 39: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 39: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 39: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 39: 39: [----------] 4 tests from UniformIntDistributionTest 39: [ RUN ] UniformIntDistributionTest.Output 39: [ OK ] UniformIntDistributionTest.Output (0 ms) 39: [ RUN ] UniformIntDistributionTest.Logical 39: [ OK ] UniformIntDistributionTest.Logical (0 ms) 39: [ RUN ] UniformIntDistributionTest.Reset 39: [ OK ] UniformIntDistributionTest.Reset (0 ms) 39: [ RUN ] UniformIntDistributionTest.AltParam 39: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 39: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 39: 39: [----------] 5 tests from UniformRealDistributionTest 39: [ RUN ] UniformRealDistributionTest.GenerateCanonical 39: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 39: [ RUN ] UniformRealDistributionTest.Output 39: [ OK ] UniformRealDistributionTest.Output (0 ms) 39: [ RUN ] UniformRealDistributionTest.Logical 39: [ OK ] UniformRealDistributionTest.Logical (0 ms) 39: [ RUN ] UniformRealDistributionTest.Reset 39: [ OK ] UniformRealDistributionTest.Reset (0 ms) 39: [ RUN ] UniformRealDistributionTest.AltParam 39: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 39: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 39: 39: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 39: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 39: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 39: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 44 tests from 10 test suites ran. (1 ms total) 39: [ PASSED ] 44 tests. 39/87 Test #39: RandomUnitTests ........................... Passed 0.09 sec test 40 Start 40: RestraintTests 40: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/RestraintTests.xml" 40: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/restraint/tests 40: Test timeout computed to be: 30 40: [==========] Running 1 test from 1 test suite. 40: [----------] Global test environment set-up. 40: [----------] 1 test from RestraintManager 40: [ RUN ] RestraintManager.restraintList 40: [ OK ] RestraintManager.restraintList (0 ms) 40: [----------] 1 test from RestraintManager (0 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 1 test from 1 test suite ran. (0 ms total) 40: [ PASSED ] 1 test. 40/87 Test #40: RestraintTests ............................ Passed 0.05 sec test 41 Start 41: TableUnitTests 41: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tables/tests 41: Test timeout computed to be: 30 41: [==========] Running 20 tests from 2 test suites. 41: [----------] Global test environment set-up. 41: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 41: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 41: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 41: [ RUN ] SplineTableTest/0.Sinc 41: [ OK ] SplineTableTest/0.Sinc (0 ms) 41: [ RUN ] SplineTableTest/0.LJ12 41: [ OK ] SplineTableTest/0.LJ12 (42 ms) 41: [ RUN ] SplineTableTest/0.PmeCorrection 41: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 41: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 41: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 41: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 41: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 41: [ RUN ] SplineTableTest/0.TwoFunctions 41: [ OK ] SplineTableTest/0.TwoFunctions (66 ms) 41: [ RUN ] SplineTableTest/0.ThreeFunctions 41: [ OK ] SplineTableTest/0.ThreeFunctions (63 ms) 41: [ RUN ] SplineTableTest/0.Simd 41: [ OK ] SplineTableTest/0.Simd (2 ms) 41: [ RUN ] SplineTableTest/0.SimdTwoFunctions 41: [ OK ] SplineTableTest/0.SimdTwoFunctions (66 ms) 41: [----------] 10 tests from SplineTableTest/0 (243 ms total) 41: 41: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 41: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 41: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 41: [ RUN ] SplineTableTest/1.Sinc 41: [ OK ] SplineTableTest/1.Sinc (0 ms) 41: [ RUN ] SplineTableTest/1.LJ12 41: [ OK ] SplineTableTest/1.LJ12 (85 ms) 41: [ RUN ] SplineTableTest/1.PmeCorrection 41: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 41: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 41: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 41: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 41: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (0 ms) 41: [ RUN ] SplineTableTest/1.TwoFunctions 41: [ OK ] SplineTableTest/1.TwoFunctions (133 ms) 41: [ RUN ] SplineTableTest/1.ThreeFunctions 41: [ OK ] SplineTableTest/1.ThreeFunctions (156 ms) 41: [ RUN ] SplineTableTest/1.Simd 41: [ OK ] SplineTableTest/1.Simd (41 ms) 41: [ RUN ] SplineTableTest/1.SimdTwoFunctions 41: [ OK ] SplineTableTest/1.SimdTwoFunctions (110 ms) 41: [----------] 10 tests from SplineTableTest/1 (529 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 20 tests from 2 test suites ran. (772 ms total) 41: [ PASSED ] 20 tests. 41/87 Test #41: TableUnitTests ............................ Passed 0.86 sec test 42 Start 42: TaskAssignmentUnitTests 42: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/taskassignment/tests 42: Test timeout computed to be: 30 42: [==========] Running 3 tests from 2 test suites. 42: [----------] Global test environment set-up. 42: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 42: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 42: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 42: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 42: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 42: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 42: 42: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 42: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 42: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (0 ms) 42: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 3 tests from 2 test suites ran. (0 ms total) 42: [ PASSED ] 3 tests. 42/87 Test #42: TaskAssignmentUnitTests ................... Passed 0.06 sec test 43 Start 43: GmxTimingTests 43: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxTimingTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/timing/tests 43: Test timeout computed to be: 30 43: [==========] Running 6 tests from 1 test suite. 43: [----------] Global test environment set-up. 43: [----------] 6 tests from TimingTest 43: [ RUN ] TimingTest.ElementCountingWorks 43: [ OK ] TimingTest.ElementCountingWorks (0 ms) 43: [ RUN ] TimingTest.ElementNoCountingWorks 43: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 43: [ RUN ] TimingTest.SubElementCountingWorks 43: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 43: [ RUN ] TimingTest.SubElementNoCountingWorks 43: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 43: [ RUN ] TimingTest.RunWallCycle 43: [ OK ] TimingTest.RunWallCycle (9 ms) 43: [ RUN ] TimingTest.RunWallCycleSub 43: [ OK ] TimingTest.RunWallCycleSub (0 ms) 43: [----------] 6 tests from TimingTest (9 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 6 tests from 1 test suite ran. (9 ms total) 43: [ PASSED ] 6 tests. 43/87 Test #43: GmxTimingTests ............................ Passed 0.06 sec test 44 Start 44: TopologyTest 44: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TopologyTest.xml" 44: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/topology/tests 44: Test timeout computed to be: 30 44: [==========] Running 153 tests from 10 test suites. 44: [----------] Global test environment set-up. 44: [----------] 3 tests from PdbAtomEntryTest 44: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 44: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 44: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 44: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 44: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 44: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 44: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 44: 44: [----------] 3 tests from ExclusionBlockTest 44: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 44: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 44: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 44: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 44: [ RUN ] ExclusionBlockTest.MergeExclusions 44: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 44: [----------] 3 tests from ExclusionBlockTest (0 ms total) 44: 44: [----------] 6 tests from InteractionListTest 44: [ RUN ] InteractionListTest.EmptyWorks 44: [ OK ] InteractionListTest.EmptyWorks (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionArray 44: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 44: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 44: [ RUN ] InteractionListTest.CanAddInteractionPointer 44: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 44: [ RUN ] InteractionListTest.CanAddListToOtherList 44: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 44: [ RUN ] InteractionListTest.ClearingWorks 44: [ OK ] InteractionListTest.ClearingWorks (0 ms) 44: [----------] 6 tests from InteractionListTest (0 ms total) 44: 44: [----------] 3 tests from IndexTest 44: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.AnalyseWorksDefaultGroups (15 ms) 44: [ RUN ] IndexTest.WriteIndexWorks 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.WriteIndexWorks (17 ms) 44: [ RUN ] IndexTest.WriteAndReadIndexWorks 44: 44: WARNING: Masses and atomic (Van der Waals) radii will be guessed 44: based on residue and atom names, since they could not be 44: definitively assigned from the information in your input 44: files. These guessed numbers might deviate from the mass 44: and radius of the atom type. Please check the output 44: files if necessary. Note, that this functionality may 44: be removed in a future GROMACS version. Please, consider 44: using another file format for your input. 44: 44: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 44: [----------] 3 tests from IndexTest (34 ms total) 44: 44: [----------] 4 tests from MtopTest 44: [ RUN ] MtopTest.RangeBasedLoop 44: [ OK ] MtopTest.RangeBasedLoop (0 ms) 44: [ RUN ] MtopTest.Operators 44: [ OK ] MtopTest.Operators (0 ms) 44: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 44: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 44: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 44: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 44: [----------] 4 tests from MtopTest (0 ms total) 44: 44: [----------] 2 tests from IListRangeTest 44: [ RUN ] IListRangeTest.RangeBasedLoopWorks 44: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 44: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 44: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 44: [----------] 2 tests from IListRangeTest (0 ms total) 44: 44: [----------] 13 tests from StringTableTest 44: [ RUN ] StringTableTest.AddSingleEntry 44: [ OK ] StringTableTest.AddSingleEntry (0 ms) 44: [ RUN ] StringTableTest.CanAccessWithAt 44: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 44: [ RUN ] StringTableTest.CanAccessWithBracket 44: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 44: [ RUN ] StringTableTest.ThrowsOutOfRange 44: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 44: [ RUN ] StringTableTest.StringCompareIsCorrect 44: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 44: [ RUN ] StringTableTest.AddTwoDistinctEntries 44: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 44: [ RUN ] StringTableTest.TryToAddDuplicates 44: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 44: [ RUN ] StringTableTest.AddLargeNumberOfEntries 44: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 44: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 44: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 44: [ RUN ] StringTableTest.CanWriteToBuffer 44: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 44: [ RUN ] StringTableTest.Roundtrip 44: [ OK ] StringTableTest.Roundtrip (0 ms) 44: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 44: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 44: [ RUN ] StringTableTest.CanCopyToLegacyTable 44: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 44: [----------] 13 tests from StringTableTest (0 ms total) 44: 44: [----------] 6 tests from LegacySymtabTest 44: [ RUN ] LegacySymtabTest.EmptyOnOpen 44: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 44: [ RUN ] LegacySymtabTest.AddSingleEntry 44: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 44: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 44: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 44: [ RUN ] LegacySymtabTest.TryToAddDuplicates 44: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 44: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 44: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 44: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 44: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 44: [----------] 6 tests from LegacySymtabTest (0 ms total) 44: 44: [----------] 5 tests from TopSortTest 44: [ RUN ] TopSortTest.WorksOnEmptyIdef 44: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 44: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 44: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 44: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 44: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 44: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 44: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 44: [----------] 5 tests from TopSortTest (0 ms total) 44: 44: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (20 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (6 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 44: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 44: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 44: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (31 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 153 tests from 10 test suites ran. (67 ms total) 44: [ PASSED ] 153 tests. 44: 44: YOU HAVE 1 DISABLED TEST 44: 44/87 Test #44: TopologyTest .............................. Passed 0.14 sec test 45 Start 45: PullTest 45: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/PullTest.xml" 45: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/tests 45: Test timeout computed to be: 30 45: [==========] Running 10 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 10 tests from PullTest 45: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 45: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 45: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 45: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 45: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 45: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 45: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 45: [ RUN ] PullTest.TransformationCoordSimple 45: [ OK ] PullTest.TransformationCoordSimple (0 ms) 45: [ RUN ] PullTest.TransformationCoordAdvanced 45: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 45: [ RUN ] PullTest.TransformationCoordTime 45: [ OK ] PullTest.TransformationCoordTime (0 ms) 45: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 45: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 45: [ RUN ] PullTest.TransformationCoordDummyExpression 45: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 45: [----------] 10 tests from PullTest (0 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 10 tests from 1 test suite ran. (0 ms total) 45: [ PASSED ] 10 tests. 45/87 Test #45: PullTest .................................. Passed 0.07 sec test 46 Start 46: SimdUnitTests 46: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 46: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/simd/tests 46: Test timeout computed to be: 30 46: [==========] Running 247 tests from 19 test suites. 46: [----------] Global test environment set-up. 46: [----------] 6 tests from SimdBootstrapTest 46: [ RUN ] SimdBootstrapTest.loadStore 46: [ OK ] SimdBootstrapTest.loadStore (0 ms) 46: [ RUN ] SimdBootstrapTest.loadU 46: [ OK ] SimdBootstrapTest.loadU (0 ms) 46: [ RUN ] SimdBootstrapTest.storeU 46: [ OK ] SimdBootstrapTest.storeU (0 ms) 46: [ RUN ] SimdBootstrapTest.loadStoreI 46: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 46: [ RUN ] SimdBootstrapTest.loadUI 46: [ OK ] SimdBootstrapTest.loadUI (0 ms) 46: [ RUN ] SimdBootstrapTest.storeUI 46: [ OK ] SimdBootstrapTest.storeUI (0 ms) 46: [----------] 6 tests from SimdBootstrapTest (0 ms total) 46: 46: [----------] 41 tests from SimdScalarTest 46: [ RUN ] SimdScalarTest.load 46: [ OK ] SimdScalarTest.load (0 ms) 46: [ RUN ] SimdScalarTest.loadU 46: [ OK ] SimdScalarTest.loadU (0 ms) 46: [ RUN ] SimdScalarTest.store 46: [ OK ] SimdScalarTest.store (0 ms) 46: [ RUN ] SimdScalarTest.storeU 46: [ OK ] SimdScalarTest.storeU (0 ms) 46: [ RUN ] SimdScalarTest.setZero 46: [ OK ] SimdScalarTest.setZero (0 ms) 46: [ RUN ] SimdScalarTest.andNot 46: [ OK ] SimdScalarTest.andNot (0 ms) 46: [ RUN ] SimdScalarTest.fma 46: [ OK ] SimdScalarTest.fma (0 ms) 46: [ RUN ] SimdScalarTest.fms 46: [ OK ] SimdScalarTest.fms (0 ms) 46: [ RUN ] SimdScalarTest.fnma 46: [ OK ] SimdScalarTest.fnma (0 ms) 46: [ RUN ] SimdScalarTest.fnms 46: [ OK ] SimdScalarTest.fnms (0 ms) 46: [ RUN ] SimdScalarTest.maskAdd 46: [ OK ] SimdScalarTest.maskAdd (0 ms) 46: [ RUN ] SimdScalarTest.maskzMul 46: [ OK ] SimdScalarTest.maskzMul (0 ms) 46: [ RUN ] SimdScalarTest.maskzFma 46: [ OK ] SimdScalarTest.maskzFma (0 ms) 46: [ RUN ] SimdScalarTest.abs 46: [ OK ] SimdScalarTest.abs (0 ms) 46: [ RUN ] SimdScalarTest.max 46: [ OK ] SimdScalarTest.max (0 ms) 46: [ RUN ] SimdScalarTest.min 46: [ OK ] SimdScalarTest.min (0 ms) 46: [ RUN ] SimdScalarTest.round 46: [ OK ] SimdScalarTest.round (0 ms) 46: [ RUN ] SimdScalarTest.trunc 46: [ OK ] SimdScalarTest.trunc (0 ms) 46: [ RUN ] SimdScalarTest.reduce 46: [ OK ] SimdScalarTest.reduce (0 ms) 46: [ RUN ] SimdScalarTest.testBits 46: [ OK ] SimdScalarTest.testBits (0 ms) 46: [ RUN ] SimdScalarTest.anyTrue 46: [ OK ] SimdScalarTest.anyTrue (0 ms) 46: [ RUN ] SimdScalarTest.selectByMask 46: [ OK ] SimdScalarTest.selectByMask (0 ms) 46: [ RUN ] SimdScalarTest.selectByNotMask 46: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 46: [ RUN ] SimdScalarTest.blend 46: [ OK ] SimdScalarTest.blend (0 ms) 46: [ RUN ] SimdScalarTest.cvtR2I 46: [ OK ] SimdScalarTest.cvtR2I (0 ms) 46: [ RUN ] SimdScalarTest.cvttR2I 46: [ OK ] SimdScalarTest.cvttR2I (0 ms) 46: [ RUN ] SimdScalarTest.cvtI2R 46: [ OK ] SimdScalarTest.cvtI2R (0 ms) 46: [ RUN ] SimdScalarTest.cvtF2D 46: [ OK ] SimdScalarTest.cvtF2D (0 ms) 46: [ RUN ] SimdScalarTest.cvtD2D 46: [ OK ] SimdScalarTest.cvtD2D (0 ms) 46: [ RUN ] SimdScalarTest.loadI 46: [ OK ] SimdScalarTest.loadI (0 ms) 46: [ RUN ] SimdScalarTest.loadUI 46: [ OK ] SimdScalarTest.loadUI (0 ms) 46: [ RUN ] SimdScalarTest.storeI 46: [ OK ] SimdScalarTest.storeI (0 ms) 46: [ RUN ] SimdScalarTest.storeUI 46: [ OK ] SimdScalarTest.storeUI (0 ms) 46: [ RUN ] SimdScalarTest.andNotI 46: [ OK ] SimdScalarTest.andNotI (0 ms) 46: [ RUN ] SimdScalarTest.testBitsI 46: [ OK ] SimdScalarTest.testBitsI (0 ms) 46: [ RUN ] SimdScalarTest.selectByMaskI 46: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 46: [ RUN ] SimdScalarTest.selectByNotMaskI 46: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 46: [ RUN ] SimdScalarTest.blendI 46: [ OK ] SimdScalarTest.blendI (0 ms) 46: [ RUN ] SimdScalarTest.cvtB2IB 46: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 46: [ RUN ] SimdScalarTest.cvtIB2B 46: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 46: [ RUN ] SimdScalarTest.expandScalarsToTriplets 46: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 46: [----------] 41 tests from SimdScalarTest (0 ms total) 46: 46: [----------] 8 tests from SimdScalarUtilTest 46: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 46: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 46: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 46: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 46: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 46: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 46: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 46: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 46: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 46: 46: [----------] 37 tests from SimdScalarMathTest 46: [ RUN ] SimdScalarMathTest.copysign 46: [ OK ] SimdScalarMathTest.copysign (0 ms) 46: [ RUN ] SimdScalarMathTest.invsqrtPair 46: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 46: [ RUN ] SimdScalarMathTest.inv 46: [ OK ] SimdScalarMathTest.inv (0 ms) 46: [ RUN ] SimdScalarMathTest.maskzInvsqrt 46: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 46: [ RUN ] SimdScalarMathTest.log 46: [ OK ] SimdScalarMathTest.log (0 ms) 46: [ RUN ] SimdScalarMathTest.exp2 46: [ OK ] SimdScalarMathTest.exp2 (0 ms) 46: [ RUN ] SimdScalarMathTest.exp 46: [ OK ] SimdScalarMathTest.exp (0 ms) 46: [ RUN ] SimdScalarMathTest.erf 46: [ OK ] SimdScalarMathTest.erf (0 ms) 46: [ RUN ] SimdScalarMathTest.erfc 46: [ OK ] SimdScalarMathTest.erfc (0 ms) 46: [ RUN ] SimdScalarMathTest.sincos 46: [ OK ] SimdScalarMathTest.sincos (0 ms) 46: [ RUN ] SimdScalarMathTest.sin 46: [ OK ] SimdScalarMathTest.sin (0 ms) 46: [ RUN ] SimdScalarMathTest.cos 46: [ OK ] SimdScalarMathTest.cos (0 ms) 46: [ RUN ] SimdScalarMathTest.tan 46: [ OK ] SimdScalarMathTest.tan (0 ms) 46: [ RUN ] SimdScalarMathTest.asin 46: [ OK ] SimdScalarMathTest.asin (0 ms) 46: [ RUN ] SimdScalarMathTest.acos 46: [ OK ] SimdScalarMathTest.acos (0 ms) 46: [ RUN ] SimdScalarMathTest.atan 46: [ OK ] SimdScalarMathTest.atan (0 ms) 46: [ RUN ] SimdScalarMathTest.atan2 46: [ OK ] SimdScalarMathTest.atan2 (0 ms) 46: [ RUN ] SimdScalarMathTest.pmeForceCorrection 46: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 46: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 46: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 46: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 46: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.invSingleAccuracy 46: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 46: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.logSingleAccuracy 46: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 46: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.expSingleAccuracy 46: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 46: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 46: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 46: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 46: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 46: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 46: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 46: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 46: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 46: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 46: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 46: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 46: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 46: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 46: [----------] 37 tests from SimdScalarMathTest (0 ms total) 46: 46: [----------] 1 test from SimdTest 46: [ RUN ] SimdTest.GmxAligned 46: [ OK ] SimdTest.GmxAligned (0 ms) 46: [----------] 1 test from SimdTest (0 ms total) 46: 46: [----------] 42 tests from SimdFloatingpointTest 46: [ RUN ] SimdFloatingpointTest.setZero 46: [ OK ] SimdFloatingpointTest.setZero (0 ms) 46: [ RUN ] SimdFloatingpointTest.set 46: [ OK ] SimdFloatingpointTest.set (0 ms) 46: [ RUN ] SimdFloatingpointTest.add 46: [ OK ] SimdFloatingpointTest.add (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskAdd 46: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 46: [ RUN ] SimdFloatingpointTest.sub 46: [ OK ] SimdFloatingpointTest.sub (0 ms) 46: [ RUN ] SimdFloatingpointTest.mul 46: [ OK ] SimdFloatingpointTest.mul (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzMul 46: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 46: [ RUN ] SimdFloatingpointTest.fma 46: [ OK ] SimdFloatingpointTest.fma (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzFma 46: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 46: [ RUN ] SimdFloatingpointTest.fms 46: [ OK ] SimdFloatingpointTest.fms (0 ms) 46: [ RUN ] SimdFloatingpointTest.fnma 46: [ OK ] SimdFloatingpointTest.fnma (0 ms) 46: [ RUN ] SimdFloatingpointTest.fnms 46: [ OK ] SimdFloatingpointTest.fnms (0 ms) 46: [ RUN ] SimdFloatingpointTest.abs 46: [ OK ] SimdFloatingpointTest.abs (0 ms) 46: [ RUN ] SimdFloatingpointTest.neg 46: [ OK ] SimdFloatingpointTest.neg (0 ms) 46: [ RUN ] SimdFloatingpointTest.and 46: [ OK ] SimdFloatingpointTest.and (0 ms) 46: [ RUN ] SimdFloatingpointTest.or 46: [ OK ] SimdFloatingpointTest.or (0 ms) 46: [ RUN ] SimdFloatingpointTest.xor 46: [ OK ] SimdFloatingpointTest.xor (0 ms) 46: [ RUN ] SimdFloatingpointTest.andNot 46: [ OK ] SimdFloatingpointTest.andNot (0 ms) 46: [ RUN ] SimdFloatingpointTest.max 46: [ OK ] SimdFloatingpointTest.max (0 ms) 46: [ RUN ] SimdFloatingpointTest.min 46: [ OK ] SimdFloatingpointTest.min (0 ms) 46: [ RUN ] SimdFloatingpointTest.round 46: [ OK ] SimdFloatingpointTest.round (0 ms) 46: [ RUN ] SimdFloatingpointTest.roundMode 46: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 46: [ RUN ] SimdFloatingpointTest.trunc 46: [ OK ] SimdFloatingpointTest.trunc (0 ms) 46: [ RUN ] SimdFloatingpointTest.frexp 46: [ OK ] SimdFloatingpointTest.frexp (0 ms) 46: [ RUN ] SimdFloatingpointTest.ldexp 46: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 46: [ RUN ] SimdFloatingpointTest.rsqrt 46: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzRsqrt 46: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 46: [ RUN ] SimdFloatingpointTest.rcp 46: [ OK ] SimdFloatingpointTest.rcp (0 ms) 46: [ RUN ] SimdFloatingpointTest.maskzRcp 46: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 46: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 46: [ RUN ] SimdFloatingpointTest.selectByNotMask 46: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpNe 46: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpLe 46: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 46: [ RUN ] SimdFloatingpointTest.cmpLt 46: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 46: [ RUN ] SimdFloatingpointTest.testBits 46: [ OK ] SimdFloatingpointTest.testBits (0 ms) 46: [ RUN ] SimdFloatingpointTest.andB 46: [ OK ] SimdFloatingpointTest.andB (0 ms) 46: [ RUN ] SimdFloatingpointTest.orB 46: [ OK ] SimdFloatingpointTest.orB (0 ms) 46: [ RUN ] SimdFloatingpointTest.anyTrueB 46: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 46: [ RUN ] SimdFloatingpointTest.blend 46: [ OK ] SimdFloatingpointTest.blend (0 ms) 46: [ RUN ] SimdFloatingpointTest.reduce 46: [ OK ] SimdFloatingpointTest.reduce (0 ms) 46: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 46: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 46: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 46: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 46: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 46: 46: [----------] 13 tests from SimdFloatingpointUtilTest 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 46: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 46: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 46: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 46: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 46: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 46: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 46: 46: [----------] 23 tests from SimdIntegerTest 46: [ RUN ] SimdIntegerTest.setZero 46: [ OK ] SimdIntegerTest.setZero (0 ms) 46: [ RUN ] SimdIntegerTest.set 46: [ OK ] SimdIntegerTest.set (0 ms) 46: [ RUN ] SimdIntegerTest.add 46: [ OK ] SimdIntegerTest.add (0 ms) 46: [ RUN ] SimdIntegerTest.sub 46: [ OK ] SimdIntegerTest.sub (0 ms) 46: [ RUN ] SimdIntegerTest.mul 46: [ OK ] SimdIntegerTest.mul (0 ms) 46: [ RUN ] SimdIntegerTest.and 46: [ OK ] SimdIntegerTest.and (0 ms) 46: [ RUN ] SimdIntegerTest.andNot 46: [ OK ] SimdIntegerTest.andNot (0 ms) 46: [ RUN ] SimdIntegerTest.or 46: [ OK ] SimdIntegerTest.or (0 ms) 46: [ RUN ] SimdIntegerTest.xor 46: [ OK ] SimdIntegerTest.xor (0 ms) 46: [ RUN ] SimdIntegerTest.extract 46: [ OK ] SimdIntegerTest.extract (0 ms) 46: [ RUN ] SimdIntegerTest.cvtR2I 46: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 46: [ RUN ] SimdIntegerTest.cvttR2I 46: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 46: [ RUN ] SimdIntegerTest.cvtI2R 46: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 46: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 46: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 46: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 46: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 46: [ RUN ] SimdIntegerTest.cmpLt 46: [ OK ] SimdIntegerTest.cmpLt (0 ms) 46: [ RUN ] SimdIntegerTest.testBits 46: [ OK ] SimdIntegerTest.testBits (0 ms) 46: [ RUN ] SimdIntegerTest.andB 46: [ OK ] SimdIntegerTest.andB (0 ms) 46: [ RUN ] SimdIntegerTest.orB 46: [ OK ] SimdIntegerTest.orB (0 ms) 46: [ RUN ] SimdIntegerTest.anyTrue 46: [ OK ] SimdIntegerTest.anyTrue (0 ms) 46: [ RUN ] SimdIntegerTest.blend 46: [ OK ] SimdIntegerTest.blend (0 ms) 46: [ RUN ] SimdIntegerTest.cvtB2IB 46: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 46: [ RUN ] SimdIntegerTest.cvtIB2B 46: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 46: [----------] 23 tests from SimdIntegerTest (0 ms total) 46: 46: [----------] 56 tests from SimdMathTest 46: [ RUN ] SimdMathTest.generateTestPointsDouble 46: [ OK ] SimdMathTest.generateTestPointsDouble (22 ms) 46: [ RUN ] SimdMathTest.copysign 46: [ OK ] SimdMathTest.copysign (0 ms) 46: [ RUN ] SimdMathTest.invsqrt 46: [ OK ] SimdMathTest.invsqrt (0 ms) 46: [ RUN ] SimdMathTest.maskzInvsqrt 46: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 46: [ RUN ] SimdMathTest.invsqrtPair 46: [ OK ] SimdMathTest.invsqrtPair (0 ms) 46: [ RUN ] SimdMathTest.sqrt 46: [ OK ] SimdMathTest.sqrt (0 ms) 46: [ RUN ] SimdMathTest.sqrtUnsafe 46: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 46: [ RUN ] SimdMathTest.inv 46: [ OK ] SimdMathTest.inv (0 ms) 46: [ RUN ] SimdMathTest.maskzInv 46: [ OK ] SimdMathTest.maskzInv (0 ms) 46: [ RUN ] SimdMathTest.cbrt 46: [ OK ] SimdMathTest.cbrt (0 ms) 46: [ RUN ] SimdMathTest.invcbrt 46: [ OK ] SimdMathTest.invcbrt (0 ms) 46: [ RUN ] SimdMathTest.log2 46: [ OK ] SimdMathTest.log2 (0 ms) 46: [ RUN ] SimdMathTest.log 46: [ OK ] SimdMathTest.log (0 ms) 46: [ RUN ] SimdMathTest.exp2 46: [ OK ] SimdMathTest.exp2 (0 ms) 46: [ RUN ] SimdMathTest.exp2Unsafe 46: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 46: [ RUN ] SimdMathTest.exp 46: [ OK ] SimdMathTest.exp (13 ms) 46: [ RUN ] SimdMathTest.expUnsafe 46: [ OK ] SimdMathTest.expUnsafe (0 ms) 46: [ RUN ] SimdMathTest.pow 46: [ OK ] SimdMathTest.pow (0 ms) 46: [ RUN ] SimdMathTest.powUnsafe 46: [ OK ] SimdMathTest.powUnsafe (0 ms) 46: [ RUN ] SimdMathTest.erf 46: [ OK ] SimdMathTest.erf (0 ms) 46: [ RUN ] SimdMathTest.erfc 46: [ OK ] SimdMathTest.erfc (0 ms) 46: [ RUN ] SimdMathTest.sin 46: [ OK ] SimdMathTest.sin (0 ms) 46: [ RUN ] SimdMathTest.cos 46: [ OK ] SimdMathTest.cos (0 ms) 46: [ RUN ] SimdMathTest.tan 46: [ OK ] SimdMathTest.tan (0 ms) 46: [ RUN ] SimdMathTest.asin 46: [ OK ] SimdMathTest.asin (0 ms) 46: [ RUN ] SimdMathTest.acos 46: [ OK ] SimdMathTest.acos (8 ms) 46: [ RUN ] SimdMathTest.atan 46: [ OK ] SimdMathTest.atan (0 ms) 46: [ RUN ] SimdMathTest.atan2 46: [ OK ] SimdMathTest.atan2 (0 ms) 46: [ RUN ] SimdMathTest.pmeForceCorrection 46: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 46: [ RUN ] SimdMathTest.pmePotentialCorrection 46: [ OK ] SimdMathTest.pmePotentialCorrection (0 ms) 46: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 46: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 46: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sqrtSingleAccuracy 46: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.invSingleAccuracy 46: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.cbrtSingleAccuracy 46: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 46: [ OK ] SimdMathTest.invcbrtSingleAccuracy (2 ms) 46: [ RUN ] SimdMathTest.log2SingleAccuracy 46: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.logSingleAccuracy 46: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.exp2SingleAccuracy 46: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 46: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.expSingleAccuracy 46: [ OK ] SimdMathTest.expSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.powSingleAccuracy 46: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 46: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 46: [ RUN ] SimdMathTest.erfSingleAccuracy 46: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.erfcSingleAccuracy 46: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.sinSingleAccuracy 46: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.cosSingleAccuracy 46: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.tanSingleAccuracy 46: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.asinSingleAccuracy 46: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.acosSingleAccuracy 46: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.atanSingleAccuracy 46: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.atan2SingleAccuracy 46: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 46: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 46: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (12 ms) 46: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 46: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 46: [----------] 56 tests from SimdMathTest (77 ms total) 46: 46: [----------] 1 test from EmptyArrayRefTest 46: [ RUN ] EmptyArrayRefTest.IsEmpty 46: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 46: [----------] 1 test from EmptyArrayRefTest (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 46: 46: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 46: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 46: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 46: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 46: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 46: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 46: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 46: 46: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefReadWriteTest/0.Assignment 46: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 46: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 46: 46: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefReadWriteTest/1.Assignment 46: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 46: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 46: 46: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefArithmeticTest/0.Basic 46: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 46: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 46: 46: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 46: [ RUN ] ArrayRefArithmeticTest/1.Basic 46: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 46: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 46: 46: [----------] 3 tests from SimdVectorOperationsTest 46: [ RUN ] SimdVectorOperationsTest.iprod 46: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 46: [ RUN ] SimdVectorOperationsTest.norm2 46: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 46: [ RUN ] SimdVectorOperationsTest.cprod 46: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 46: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 247 tests from 19 test suites ran. (78 ms total) 46: [ PASSED ] 247 tests. 46/87 Test #46: SimdUnitTests ............................. Passed 0.12 sec test 47 Start 47: CompatibilityHelpersTests 47: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 47: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/compat/tests 47: Test timeout computed to be: 30 47: [==========] Running 9 tests from 6 test suites. 47: [----------] Global test environment set-up. 47: [----------] 4 tests from TemplateMPTest 47: [ RUN ] TemplateMPTest.MpWithIndexInt 47: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexIntBad 47: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexBool 47: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 47: [ RUN ] TemplateMPTest.MpWithIndexEnum 47: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 47: [----------] 4 tests from TemplateMPTest (0 ms total) 47: 47: [----------] 1 test from NotNullConstruction 47: [ RUN ] NotNullConstruction.Works 47: [ OK ] NotNullConstruction.Works (0 ms) 47: [----------] 1 test from NotNullConstruction (0 ms total) 47: 47: [----------] 1 test from NotNullCasting 47: [ RUN ] NotNullCasting.Works 47: [ OK ] NotNullCasting.Works (0 ms) 47: [----------] 1 test from NotNullCasting (0 ms total) 47: 47: [----------] 1 test from NotNullAssignment 47: [ RUN ] NotNullAssignment.Works 47: [ OK ] NotNullAssignment.Works (0 ms) 47: [----------] 1 test from NotNullAssignment (0 ms total) 47: 47: [----------] 1 test from MakeNotNull 47: [ RUN ] MakeNotNull.Works 47: [ OK ] MakeNotNull.Works (0 ms) 47: [----------] 1 test from MakeNotNull (0 ms total) 47: 47: [----------] 1 test from NotNull 47: [ RUN ] NotNull.WorksInContainers 47: [ OK ] NotNull.WorksInContainers (0 ms) 47: [----------] 1 test from NotNull (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 9 tests from 6 test suites ran. (0 ms total) 47: [ PASSED ] 9 tests. 47/87 Test #47: CompatibilityHelpersTests ................. Passed 0.05 sec test 48 Start 48: GmxAnaTest 48: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 48: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxana/tests 48: Test timeout computed to be: 600 48: [==========] Running 31 tests from 4 test suites. 48: [----------] Global test environment set-up. 48: [----------] 7 tests from Entropy 48: [ RUN ] Entropy.Schlitter_300_NoLinear 48: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 48: [ RUN ] Entropy.Schlitter_300_Linear 48: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 48: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 48: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 48: [ RUN ] Entropy.QuasiHarmonic_200_Linear 48: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 48: [ RUN ] Entropy.EntropyCompare_200_Linear 48: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 48: [ RUN ] Entropy.EntropyCompare_300_Linear 48: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 48: [----------] 7 tests from Entropy (0 ms total) 48: 48: [----------] 2 tests from GmxChiTest 48: [ RUN ] GmxChiTest.gmxchiWorksWithAll 48: Analyzing from residue 1 to residue 11 48: 10 residues with dihedrals found 48: 46 dihedrals found 48: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 48: j after resetting (nr. active dihedrals) = 46 48: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 48: Now calculating transitions... 48: Total number of transitions: 0 48: Now printing out transitions and OPs... 48: Now printing out rotamer occupancies... 48: Now calculating Chi product trajectories... 48: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 48: [ OK ] GmxChiTest.gmxchiWorksWithAll (1771 ms) 48: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 48: Analyzing from residue 2 to residue 6 48: 5 residues with dihedrals found 48: 23 dihedrals found 48: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 48: j after resetting (nr. active dihedrals) = 23 48: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 48: Now calculating transitions... 48: Total number of transitions: 0 48: Now printing out transitions and OPs... 48: Now printing out rotamer occupancies... 48: Now calculating Chi product trajectories... 48: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 48: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (884 ms) 48: [----------] 2 tests from GmxChiTest (2952 ms total) 48: 48: [----------] 10 tests from MindistTest 48: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistWorksWithSingleAtoms (22 ms) 48: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 2: 'atom3' 48: Selected 3: 'atoms12' 48: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 48: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 48: [ RUN ] MindistTest.mindistPicksUpContacts 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 48: [ RUN ] MindistTest.ngWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.ngWorks (0 ms) 48: [ RUN ] MindistTest.groupWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 3: 'atoms12' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.groupWorks (0 ms) 48: [ RUN ] MindistTest.maxDistWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 2: 'atom3' 48: Selected 3: 'atoms12' 48: [ OK ] MindistTest.maxDistWorks (8 ms) 48: [ RUN ] MindistTest.noPbcWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 0: 'atom1' 48: Selected 1: 'atom2' 48: [ OK ] MindistTest.noPbcWorks (0 ms) 48: [ RUN ] MindistTest.resPerTimeWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 3: 'atoms12' 48: Selected 2: 'atom3' 48: [ OK ] MindistTest.resPerTimeWorks (0 ms) 48: [ RUN ] MindistTest.matrixWorks 48: Group 0 ( atom1) has 1 elements 48: Group 1 ( atom2) has 1 elements 48: Group 2 ( atom3) has 1 elements 48: Group 3 ( atoms12) has 2 elements 48: Group 4 ( atoms23) has 2 elements 48: Group 5 ( atoms123) has 3 elements 48: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 48: Reading frame 0 time 0.000 Last frame 0 time 0.000 48: Selected 5: 'atoms123' 48: Special case: making distance matrix between all atoms in group atoms123 48: [ OK ] MindistTest.matrixWorks (0 ms) 48: [----------] 10 tests from MindistTest (34 ms total) 48: 48: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: trr version: GMX_trn_file (single precision) 48: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (0 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 48: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (8 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (1 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (9 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 48: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (1 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (0 ms) 48: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 48: Group 0 ( System) has 6 elements 48: Group 1 ( Water) has 6 elements 48: Group 2 ( SOL) has 6 elements 48: Select a group: Reading frame 0 time 0.000 48: WARNING: If there are molecules in the input trajectory file 48: that are broken across periodic boundaries, they 48: cannot be made whole (or treated as whole) without 48: you providing a run input file. 48: 48: Reading frame 1 time 1.000 Last frame 1 time 1.000 48: 48: WARNING: Masses and atomic (Van der Waals) radii will be guessed 48: based on residue and atom names, since they could not be 48: definitively assigned from the information in your input 48: files. These guessed numbers might deviate from the mass 48: and radius of the atom type. Please check the output 48: files if necessary. Note, that this functionality may 48: be removed in a future GROMACS version. Please, consider 48: using another file format for your input. 48: 48: Selected 0: 'System' 48: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (9 ms) 48: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (35 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 31 tests from 4 test suites ran. (3022 ms total) 48: [ PASSED ] 31 tests. 48/87 Test #48: GmxAnaTest ................................ Passed 3.10 sec test 49 Start 49: GmxPreprocessTests 49: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests 49: Test timeout computed to be: 1920 49: [==========] Running 93 tests from 12 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from GenconfTest 49: [ RUN ] GenconfTest.nbox_Works 49: [ OK ] GenconfTest.nbox_Works (0 ms) 49: [ RUN ] GenconfTest.nbox_norenumber_Works 49: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 49: [ RUN ] GenconfTest.nbox_dist_Works 49: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 49: [ RUN ] GenconfTest.nbox_rot_Works 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: center of geometry: 1.733667, 1.477000, 0.905167 49: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 49: [----------] 4 tests from GenconfTest (3 ms total) 49: 49: [----------] 2 tests from GenionTest 49: [ RUN ] GenionTest.HighConcentrationIonPlacement 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 49: buffer. The cluster pair list does have a buffering effect, but choosing 49: a larger rlist might be necessary for good energy conservation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 49: < 0 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: Generating 1-4 interactions: fudge = 0.5 49: Number of degrees of freedom in T-Coupling group rest is 1308.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: Group 0 ( System) has 653 elements 49: Group 1 ( Water) has 648 elements 49: Group 2 ( SOL) has 648 elements 49: Group 3 ( non-Water) has 5 elements 49: Group 4 ( Other) has 5 elements 49: Group 5 ( METH) has 5 elements 49: Select a group: Number of (3-atomic) solvent molecules: 216 49: Using random seed 1997. 49: Replacing solvent molecule 56 (atom 168) with NA 49: Replacing solvent molecule 120 (atom 360) with NA 49: Replacing solvent molecule 182 (atom 546) with NA 49: Replacing solvent molecule 71 (atom 213) with NA 49: Replacing solvent molecule 189 (atom 567) with CL 49: Replacing solvent molecule 54 (atom 162) with CL 49: Replacing solvent molecule 155 (atom 465) with CL 49: Replacing solvent molecule 99 (atom 297) with CL 49: 49: Setting the LD random seed to 2044651575 49: 49: Generated 331705 of the 331705 non-bonded parameter combinations 49: 49: Generated 331705 of the 331705 1-4 parameter combinations 49: 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: 49: Excluding 3 bonded neighbours molecule type 'methane' 49: Analysing residue names: 49: There are: 216 Water residues 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: This run will generate roughly 0 Mb of data 49: Will try to add 4 NA ions and 4 CL ions. 49: Select a continuous group of solvent molecules 49: Selected 1: 'Water' 49: [ OK ] GenionTest.HighConcentrationIonPlacement (839 ms) 49: [ RUN ] GenionTest.NoIonPlacement 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 49: buffer. The cluster pair list does have a buffering effect, but choosing 49: a larger rlist might be necessary for good energy conservation. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 49: < 0 49: 49: 49: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: Generating 1-4 interactions: fudge = 0.5 49: Number of degrees of freedom in T-Coupling group rest is 1308.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 49: You are using a plain Coulomb cut-off, which might produce artifacts. 49: You might want to consider using PME electrostatics. 49: 49: 49: 49: There were 4 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: No ions to add, will just copy input configuration. 49: Setting the LD random seed to -135266317 49: 49: Generated 331705 of the 331705 non-bonded parameter combinations 49: 49: Generated 331705 of the 331705 1-4 parameter combinations 49: 49: Excluding 2 bonded neighbours molecule type 'SOL' 49: 49: Excluding 3 bonded neighbours molecule type 'methane' 49: Analysing residue names: 49: There are: 216 Water residues 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: This run will generate roughly 0 Mb of data 49: [ OK ] GenionTest.NoIonPlacement (836 ms) 49: [----------] 2 tests from GenionTest (1676 ms total) 49: 49: [----------] 1 test from GenRestrTest 49: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 49: 49: Reading structure file 49: Group 0 ( System) has 156 elements 49: Group 1 ( Protein) has 156 elements 49: Group 2 ( Protein-H) has 75 elements 49: Group 3 ( C-alpha) has 10 elements 49: Group 4 ( Backbone) has 30 elements 49: Group 5 ( MainChain) has 40 elements 49: Group 6 ( MainChain+Cb) has 49 elements 49: Group 7 ( MainChain+H) has 52 elements 49: Group 8 ( SideChain) has 104 elements 49: Group 9 ( SideChain-H) has 35 elements 49: Select a group: Select group to position restrain 49: Selected 3: 'C-alpha' 49: [ OK ] GenRestrTest.SimpleRestraintsGenerated (0 ms) 49: [----------] 1 test from GenRestrTest (0 ms total) 49: 49: [----------] 9 tests from PreprocessingAtomTypesTest 49: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 49: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 49: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 49: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 49: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 49: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 49: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 49: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 49: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 49: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 49: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 49: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 49: 49: [----------] 10 tests from PreprocessingBondAtomTypeTest 49: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 49: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 49: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 49: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 49: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 49: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 49: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 49: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 49: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 49: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 49: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 49: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 49: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 49: 49: [----------] 1 test from GromppDirectiveTest 49: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 49: Ignoring obsolete mdp entry 'title' 49: Generating 1-4 interactions: fudge = 0.5 49: 49: NOTE 1 [file directives.top, line 44]: 49: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 49: any other atom in the same moleculetype. Although technically this might 49: not cause issues in a simulation, this often means that the user forgot 49: to add a bond/potential/constraint or put multiple molecules in the same 49: moleculetype definition by mistake. Run with -v to get information for 49: each atom. 49: 49: Number of degrees of freedom in T-Coupling group rest is 9.00 49: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 49: NVE simulation: will use the initial temperature of 300.000 K for 49: determining the Verlet buffer size 49: 49: 49: There were 2 NOTEs 49: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 49: Setting the LD random seed to -2177 49: 49: Generated 10 of the 10 non-bonded parameter combinations 49: 49: Generated 10 of the 10 1-4 parameter combinations 49: 49: Excluding 0 bonded neighbours molecule type 'A' 49: 49: Setting gen_seed to -287838213 49: 49: Velocities were taken from a Maxwell distribution at 300 K 49: Analysing residue names: 49: There are: 1 Other residues 49: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 49: 49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 49: 49: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 49: 49: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 49: 49: Note that mdrun will redetermine rlist based on the actual pair-list setup 49: 49: This run will generate roughly 0 Mb of data 49: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (10 ms) 49: [----------] 1 test from GromppDirectiveTest (10 ms total) 49: 49: [----------] 5 tests from InsertMoleculesTest 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 8 atoms)! 49: 49: Added 1 molecules (out of 1 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 49: 49: Output configuration contains 8 atoms in 4 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (1 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 2 atoms)! 49: Try 2 success (now 4 atoms)! 49: Try 3 success (now 6 atoms)! 49: Try 4 success (now 8 atoms)! 49: Try 5 success (now 10 atoms)! 49: 49: Added 5 molecules (out of 5 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 49: 49: Output configuration contains 10 atoms in 10 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (0 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 8 atoms)! 49: Try 2 success (now 10 atoms)! 49: 49: Added 2 molecules (out of 2 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 49: 49: Output configuration contains 10 atoms in 4 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (8 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 49: Reading solute configuration 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Try 1 success (now 650 atoms)! 49: Try 2 success (now 652 atoms)! 49: Try 3 success (now 654 atoms)! 49: Try 4 success (now 656 atoms)! 49: 49: Added 4 molecules (out of 4 requested) 49: Replaced 8 residues (24 atoms) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 49: 49: Output configuration contains 632 atoms in 212 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (2 ms) 49: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Using random seed 1997 49: Read 4 positions from file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 49: 49: Try 1 success (now 2 atoms)! 49: Try 2 success (now 4 atoms)! 49: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 49: Try 13 success (now 6 atoms)! 49: 49: Added 3 molecules (out of 4 requested) 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 49: 49: Output configuration contains 6 atoms in 3 residues 49: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (12 ms) 49: [----------] 5 tests from InsertMoleculesTest (26 ms total) 49: 49: [----------] 3 tests from MassRepartitioning 49: [ RUN ] MassRepartitioning.ValidCaseWorks 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 49: [ RUN ] MassRepartitioning.UnboundGivesWarning 49: 49: WARNING 1 [file unknown]: 49: The are 1 atoms that have a mass below the mass repartitioning limit but 49: are not bound. These masses cannot be repartitioned. 49: 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 49: [ RUN ] MassRepartitioning.LightPartnerGivesError 49: 49: ERROR 1 [file unknown]: 49: Light atoms are bound to at least one atom that has a too low mass for 49: repartioning 49: 49: The smallest mass in the system is 2, setting the minimum mass to 6 49: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 49: [----------] 3 tests from MassRepartitioning (0 ms total) 49: 49: [----------] 35 tests from GetIrTest 49: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 49: Ignoring obsolete mdp entry 'title' 49: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (1 ms) 49: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 49: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (50 ms) 49: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsKeyWithoutValue (1 ms) 49: [ RUN ] GetIrTest.RejectsValueWithoutKey 49: [ OK ] GetIrTest.RejectsValueWithoutKey (37 ms) 49: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 49: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (17 ms) 49: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) 49: [ RUN ] GetIrTest.AcceptsEmptyLines 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsEmptyLines (1 ms) 49: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 49: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 49: [ RUN ] GetIrTest.MtsCheckNstenergy 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstenergy (5) 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 49: [ RUN ] GetIrTest.MtsCheckNstpcouple 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 49: Pressure coupling incorrect number of values (I need exactly 1) 49: 49: 49: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 49: Pressure coupling incorrect number of values (I need exactly 1) 49: 49: 49: ERROR 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: With multiple time stepping, nstpcouple should be a multiple of 49: mts-factor 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: 49: ERROR 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: The Berendsen barostat does not generate any strictly correct ensemble, 49: and should not be used for new production simulations (in our opinion). 49: We recommend using the C-rescale barostat instead. 49: 49: 49: ERROR 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 49: compressibility must be > 0 when using pressure coupling Berendsen 49: 49: 49: [ OK ] GetIrTest.MtsCheckNstpcouple (13 ms) 49: [ RUN ] GetIrTest.MtsCheckNstdhdl 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: Setting nstcalcenergy (100) equal to nstdhdl (5) 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: 49: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 49: Lambda state must be set, either with init-lambda-state or with 49: init-lambda 49: 49: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 49: [ RUN ] GetIrTest.MtsCheckSDNotSupported 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 49: Multiple time stepping is only supported with integrator md 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 49: [ RUN ] GetIrTest.AcceptsElectricField 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricField (9 ms) 49: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 49: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (5 ms) 49: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 49: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (32 ms) 49: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) 49: [ RUN ] GetIrTest.RejectsImplicitSolventYes 49: [ OK ] GetIrTest.RejectsImplicitSolventYes (34 ms) 49: [ RUN ] GetIrTest.AcceptsMimic 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsMimic (1 ms) 49: [ RUN ] GetIrTest.AcceptsTransformationCoord 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 49: pull-coord2 has a non-zero force constant and is also referenced in 49: pull-coord1-expression. Make sure that this is intended. In most use 49: cases, the pull coordinates referenced by a transformation coordinate 49: should have their force constant set to zero. 49: 49: 49: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.AcceptsTransformationCoord (1 ms) 49: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 49: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (9 ms) 49: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 49: pull-coord2 can not use pull-coord1 in the transformation since this is a 49: constraint 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 49: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 49: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 49: 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (2 ms) 49: [ RUN ] GetIrTest.MissingTransformationCoordExpression 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 49: pull-coord1-expression not set for pull coordinate of geometry 49: 'transformation' 49: 49: 49: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 49: For a correct single-point energy evaluation with nsteps = 0, use 49: continuation = yes to avoid constraining the input coordinates. 49: 49: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 49: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 49: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 49: in total 100001 steps. This is not compatible with using soft-core 49: potentials. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (13 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 49: won't change anymore after step 100000 until the end of the simulation 49: after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 49: won't change anymore after step 100000 until the end of the simulation 49: after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 49: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 49: components won't change anymore after step 100000 until the end of the 49: simulation after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (9 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 49: 49: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 49: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 49: components won't change anymore after step 100000 until the end of the 49: simulation after 100001 steps. 49: 49: 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 49: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 49: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (17 ms) 49: [----------] 35 tests from GetIrTest (284 ms total) 49: 49: [----------] 6 tests from SolvateTest 49: [ RUN ] SolvateTest.cs_box_Works 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 1x1x1 boxes 49: Solvent box contains 270 atoms in 90 residues 49: Removed 129 solvent atoms due to solvent-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 47 residues 49: Generated solvent containing 141 atoms in 47 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 49: 49: Output configuration contains 141 atoms in 47 residues 49: Volume : 1.331 (nm^3) 49: Density : 1056.36 (g/l) 49: Number of solvent molecules: 47 49: 49: [ OK ] SolvateTest.cs_box_Works (2 ms) 49: [ RUN ] SolvateTest.cs_cp_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 886 residues 49: Generated solvent containing 2658 atoms in 886 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 49: 49: Output configuration contains 2664 atoms in 888 residues 49: Volume : 27.2709 (nm^3) 49: Density : 974.777 (g/l) 49: Number of solvent molecules: 886 49: 49: [ OK ] SolvateTest.cs_cp_Works (71 ms) 49: [ RUN ] SolvateTest.cs_cp_p_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 886 residues 49: Generated solvent containing 2658 atoms in 886 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 49: 49: Output configuration contains 2664 atoms in 888 residues 49: Volume : 27.2709 (nm^3) 49: Density : 974.777 (g/l) 49: Number of solvent molecules: 886 49: 49: Processing topology 49: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 49: [ OK ] SolvateTest.cs_cp_p_Works (51 ms) 49: [ RUN ] SolvateTest.shell_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 3660 atoms in 1220 residues 49: Removed 987 solvent atoms due to solvent-solvent overlap 49: Removed 1902 solvent atoms more than 1.000000 nm from solute. 49: Removed 15 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 252 residues 49: Generated solvent containing 756 atoms in 252 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 49: 49: Output configuration contains 762 atoms in 254 residues 49: Volume : 27.2709 (nm^3) 49: Density : 279.3 (g/l) 49: Number of solvent molecules: 252 49: 49: [ OK ] SolvateTest.shell_Works (39 ms) 49: [ RUN ] SolvateTest.update_Topology_Works 49: Reading solute configuration 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 3x3x3 boxes 49: Solvent box contains 14952 atoms in 4984 residues 49: Removed 2787 solvent atoms due to solvent-solvent overlap 49: Removed 30 solvent atoms due to solute-solvent overlap 49: Sorting configuration 49: Found 2 different molecule types: 49: HOH ( 3 atoms): 1876 residues 49: SOL ( 3 atoms): 2169 residues 49: Generated solvent containing 0 atoms in 0 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 49: 49: Output configuration contains 12141 atoms in 4047 residues 49: Volume : 125 (nm^3) 49: Density : 968.963 (g/l) 49: Number of solvent molecules: 4045 49: 49: Processing topology 49: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 49: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 49: [ OK ] SolvateTest.update_Topology_Works (211 ms) 49: [ RUN ] SolvateTest.cs_pdb_big_box_Works 49: Reading solvent configuration 49: 49: Initialising inter-atomic distances... 49: 49: WARNING: Masses and atomic (Van der Waals) radii will be guessed 49: based on residue and atom names, since they could not be 49: definitively assigned from the information in your input 49: files. These guessed numbers might deviate from the mass 49: and radius of the atom type. Please check the output 49: files if necessary. Note, that this functionality may 49: be removed in a future GROMACS version. Please, consider 49: using another file format for your input. 49: 49: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 49: from the source below. This means the results may be different 49: compared to previous GROMACS versions. 49: 49: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 49: A. Bondi 49: van der Waals Volumes and Radii 49: J. Phys. Chem. 68 (1964) pp. 441-451 49: -------- -------- --- Thank You --- -------- -------- 49: 49: Generating solvent configuration 49: Will generate new solvent configuration of 2x2x2 boxes 49: Solvent box contains 1218 atoms in 406 residues 49: Removed 555 solvent atoms due to solvent-solvent overlap 49: Sorting configuration 49: Found 1 molecule type: 49: SOL ( 3 atoms): 221 residues 49: Generated solvent containing 663 atoms in 221 residues 49: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 49: 49: Output configuration contains 663 atoms in 221 residues 49: Volume : 8 (nm^3) 49: Density : 826.409 (g/l) 49: Number of solvent molecules: 221 49: 49: [ OK ] SolvateTest.cs_pdb_big_box_Works (24 ms) 49: [----------] 6 tests from SolvateTest (401 ms total) 49: 49: [----------] 1 test from TopDirTests 49: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 49: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 49: [----------] 1 test from TopDirTests (0 ms total) 49: 49: [----------] 16 tests from CorrectVelocity/MaxwellTest 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (16 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (16 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 49: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 49: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 49: [----------] 16 tests from CorrectVelocity/MaxwellTest (40 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 93 tests from 12 test suites ran. (2444 ms total) 49: [ PASSED ] 93 tests. 49/87 Test #49: GmxPreprocessTests ........................ Passed 2.52 sec test 50 Start 50: Pdb2gmx1Test 50: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml" 50: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests 50: Test timeout computed to be: 1920 50: [==========] Running 30 tests from 1 test suite. 50: [----------] Global test environment set-up. 50: [----------] 30 tests from Oplsaa/Pdb2gmxTest 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (102 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (115 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (89 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (104 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (275 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (86 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (116 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (75 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (85 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip3p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (245 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (69 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (70 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (89 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (49 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (174 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (62 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (76 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (91 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (81 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip4p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (316 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 0 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (89 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 0 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (110 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 0 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (93 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 0 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (83 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 0 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (190 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 25 donors and 23 acceptors were found. 50: There are 41 hydrogen bonds 50: Will use HISE for residue 8 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS3 HIS8 50: SG9 NE251 50: HIS8 NE251 1.055 50: MET12 SD83 0.763 0.990 50: Marked 124 virtual sites 50: Added 16 dummy masses 50: Added 26 new constraints 50: Before cleaning: 653 pairs 50: Before cleaning: 663 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 50: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 128 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (128 atoms, 16 residues) 50: 50: Identified residue ALA2 as a starting terminus. 50: 50: Identified residue SER17 as a ending terminus. 50: Start terminus ALA-2: NH3+ 50: End terminus SER-17: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 252 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 254, now 254 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 663 dihedrals, 51 impropers, 457 angles 50: 650 pairs, 254 bonds and 130 virtual sites 50: 50: Total mass 1846.112 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (70 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 30 donors and 22 acceptors were found. 50: There are 36 hydrogen bonds 50: Will use HISE for residue 29 50: Will use HISE for residue 32 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS27 HIS29 50: SG90 NE2111 50: HIS29 NE2111 0.987 50: HIS32 NE2135 1.590 1.155 50: Marked 132 virtual sites 50: Added 10 dummy masses 50: Added 19 new constraints 50: Before cleaning: 748 pairs 50: Before cleaning: 778 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 50: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 149 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (149 atoms, 16 residues) 50: 50: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue THR18 as a starting terminus. 50: 50: Identified residue PHE33 as a ending terminus. 50: Start terminus THR-18: NH3+ 50: End terminus PHE-33: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 281 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 290, now 290 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 778 dihedrals, 72 impropers, 516 angles 50: 736 pairs, 290 bonds and 133 virtual sites 50: 50: Total mass 2088.357 a.m.u. 50: 50: Total charge 1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (76 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 22 acceptors were found. 50: There are 26 hydrogen bonds 50: Will use HISE for residue 45 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS45 50: NE295 50: MET46 SD102 1.078 50: Marked 123 virtual sites 50: Added 22 dummy masses 50: Added 35 new constraints 50: Before cleaning: 676 pairs 50: Before cleaning: 696 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 50: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 132 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (132 atoms, 16 residues) 50: 50: Identified residue ALA34 as a starting terminus. 50: 50: Identified residue ALA49 as a ending terminus. 50: Start terminus ALA-34: NH3+ 50: End terminus ALA-49: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 255 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 261, now 261 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 696 dihedrals, 56 impropers, 472 angles 50: 667 pairs, 261 bonds and 132 virtual sites 50: 50: Total mass 1861.128 a.m.u. 50: 50: Total charge -1.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (62 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 22 donors and 21 acceptors were found. 50: There are 30 hydrogen bonds 50: Will use HISE for residue 60 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: HIS60 50: NE285 50: CYS62 SG98 0.803 50: Marked 111 virtual sites 50: Added 18 dummy masses 50: Added 31 new constraints 50: Before cleaning: 603 pairs 50: Before cleaning: 618 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 50: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 50: 50: chain #res #atoms 50: 50: 1 ' ' 16 117 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 (117 atoms, 16 residues) 50: 50: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 50: 50: Identified residue LYS50 as a starting terminus. 50: 50: Identified residue PRO65 as a ending terminus. 50: Start terminus LYS-50: NH3+ 50: End terminus PRO-65: PRO-COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 16 residues with 228 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 232, now 232 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 618 dihedrals, 48 impropers, 419 angles 50: 597 pairs, 232 bonds and 116 virtual sites 50: 50: Total mass 1662.883 a.m.u. 50: 50: Total charge 0.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (61 ms) 50: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 50: All occupancies are one 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 50: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 50: Analysing hydrogen-bonding network for automated assignment of histidine 50: protonation. 89 donors and 98 acceptors were found. 50: There are 129 hydrogen bonds 50: Will use HISE for residue 31 50: Will use HISE for residue 51 50: 9 out of 9 lines of specbond.dat converted successfully 50: Special Atom Distance matrix: 50: CYS25 HIS31 HIS51 50: SG14 NE264 NE2226 50: HIS31 NE264 1.921 50: HIS51 NE2226 1.498 2.650 50: CYS80 SG477 0.207 1.984 1.570 50: Linking CYS-25 SG-14 and CYS-80 SG-477... 50: Marked 447 virtual sites 50: Added 58 dummy masses 50: Added 101 new constraints 50: Before cleaning: 2499 pairs 50: Before cleaning: 2524 dihedrals 50: Using the Oplsaa force field in directory oplsaa.ff 50: 50: going to rename oplsaa.ff/aminoacids.r2b 50: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 50: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 50: 50: Analyzing pdb file 50: Splitting chemical chains based on TER records or chain id changing. 50: 50: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 50: 50: chain #res #atoms 50: 50: 1 'A' 58 488 50: 50: All occupancies are one 50: 50: Reading residue database... (Oplsaa) 50: 50: Processing chain 1 'A' (488 atoms, 58 residues) 50: 50: Identified residue ASN24 as a starting terminus. 50: 50: Identified residue ARG81 as a ending terminus. 50: Start terminus ASN-24: NH3+ 50: End terminus ARG-81: COO- 50: 50: Checking for duplicate atoms.... 50: 50: Generating any missing hydrogen atoms and/or adding termini. 50: 50: Now there are 58 residues with 936 atoms 50: 50: Making bonds... 50: 50: Number of bonds was 951, now 951 50: 50: Generating angles, dihedrals and pairs... 50: 50: Making cmap torsions... 50: 50: There are 2524 dihedrals, 208 impropers, 1704 angles 50: 2469 pairs, 951 bonds and 462 virtual sites 50: 50: Total mass 6908.578 a.m.u. 50: 50: Total charge -6.000 e 50: 50: Writing topology 50: 50: Writing coordinate file... 50: 50: --------- PLEASE NOTE ------------ 50: 50: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 50: 50: The Oplsaa force field and the tip5p water model are used. 50: 50: --------- ETON ESAELP ------------ 50: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (205 ms) 50: [----------] 30 tests from Oplsaa/Pdb2gmxTest (3452 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 30 tests from 1 test suite ran. (3452 ms total) 50: [ PASSED ] 30 tests. 50/87 Test #50: Pdb2gmx1Test .............................. Passed 3.53 sec test 51 Start 51: Pdb2gmx2Test 51: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml" 51: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 40 tests from 2 test suites. 51: [----------] Global test environment set-up. 51: [----------] 20 tests from G43a1/Pdb2gmxTest 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (77 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (77 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (111 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (94 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (174 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 37 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 37 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (75 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 53 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 51 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (93 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 36 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 36 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (120 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 33 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 31 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (72 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 146 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 137 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (128 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (55 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (56 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (51 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (49 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (153 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 37 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 305 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 165 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 172, now 167 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 77 impropers, 241 angles 51: 267 pairs, 167 bonds and 37 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (107 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 53 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 429 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 202 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 216, now 211 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 134 impropers, 316 angles 51: 273 pairs, 211 bonds and 51 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (113 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 36 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 349 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 168 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 179, now 174 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 102 impropers, 260 angles 51: 242 pairs, 174 bonds and 36 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (108 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 33 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 299 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 150 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 159, now 154 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 80 impropers, 227 angles 51: 232 pairs, 154 bonds and 31 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (107 ms) 51: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 146 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1256 dihedrals 51: Using the Gromos43a1 force field in directory gromos43a1.ff 51: 51: going to rename gromos43a1.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos43a1) 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 635 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 655, now 650 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 350 impropers, 955 angles 51: 972 pairs, 650 bonds and 137 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos43a1 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (211 ms) 51: [----------] 20 tests from G43a1/Pdb2gmxTest (2058 ms total) 51: 51: [----------] 20 tests from G53a6/Pdb2gmxTest 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (120 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (123 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (105 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (88 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (179 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 39 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 39 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (122 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 57 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 55 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (115 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 38 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 38 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (101 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 35 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 33 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (101 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 150 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 141 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spc water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (173 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 0 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (81 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 0 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (74 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 0 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (101 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 0 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (96 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 0 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (184 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 25 donors and 23 acceptors were found. 51: There are 41 hydrogen bonds 51: Will use HISE for residue 8 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS3 HIS8 51: SG9 NE251 51: HIS8 NE251 1.055 51: MET12 SD83 0.763 0.990 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 39 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 267 pairs 51: Before cleaning: 312 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 51: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 128 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (128 atoms, 16 residues) 51: 51: Identified residue ALA2 as a starting terminus. 51: 51: Identified residue SER17 as a ending terminus. 51: Start terminus ALA-2: NH3+ 51: End terminus SER-17: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 167 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 174, now 169 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 90 dihedrals, 79 impropers, 245 angles 51: 267 pairs, 169 bonds and 39 virtual sites 51: 51: Total mass 1846.116 a.m.u. 51: 51: Total charge 0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (85 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 30 donors and 22 acceptors were found. 51: There are 36 hydrogen bonds 51: Will use HISE for residue 29 51: Will use HISE for residue 32 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS27 HIS29 51: SG90 NE2111 51: HIS29 NE2111 0.987 51: HIS32 NE2135 1.590 1.155 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 57 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 273 pairs 51: Before cleaning: 443 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 51: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 149 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (149 atoms, 16 residues) 51: 51: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue THR18 as a starting terminus. 51: 51: Identified residue PHE33 as a ending terminus. 51: Start terminus THR-18: NH3+ 51: End terminus PHE-33: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 206 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 220, now 215 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 93 dihedrals, 138 impropers, 324 angles 51: 273 pairs, 215 bonds and 55 virtual sites 51: 51: Total mass 2088.361 a.m.u. 51: 51: Total charge 1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (91 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 22 acceptors were found. 51: There are 26 hydrogen bonds 51: Will use HISE for residue 45 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS45 51: NE295 51: MET46 SD102 1.078 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 38 virtual sites 51: Added 4 dummy masses 51: Added 8 new constraints 51: 51: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 242 pairs 51: Before cleaning: 356 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 51: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 132 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (132 atoms, 16 residues) 51: 51: Identified residue ALA34 as a starting terminus. 51: 51: Identified residue ALA49 as a ending terminus. 51: Start terminus ALA-34: NH3+ 51: End terminus ALA-49: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 170 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 181, now 176 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 81 dihedrals, 104 impropers, 264 angles 51: 242 pairs, 176 bonds and 38 virtual sites 51: 51: Total mass 1861.132 a.m.u. 51: 51: Total charge -1.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (82 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 22 donors and 21 acceptors were found. 51: There are 30 hydrogen bonds 51: Will use HISE for residue 60 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: HIS60 51: NE285 51: CYS62 SG98 0.803 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 35 virtual sites 51: Added 4 dummy masses 51: Added 10 new constraints 51: 51: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 232 pairs 51: Before cleaning: 306 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 51: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 51: 51: chain #res #atoms 51: 51: 1 ' ' 16 117 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 (117 atoms, 16 residues) 51: 51: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 51: 51: Identified residue LYS50 as a starting terminus. 51: 51: Identified residue PRO65 as a ending terminus. 51: Start terminus LYS-50: NH3+ 51: End terminus PRO-65: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 16 residues with 152 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 161, now 156 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 78 dihedrals, 82 impropers, 231 angles 51: 232 pairs, 156 bonds and 33 virtual sites 51: 51: Total mass 1662.887 a.m.u. 51: 51: Total charge -0.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (82 ms) 51: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 51: All occupancies are one 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 51: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 51: Analysing hydrogen-bonding network for automated assignment of histidine 51: protonation. 89 donors and 98 acceptors were found. 51: There are 129 hydrogen bonds 51: Will use HISE for residue 31 51: Will use HISE for residue 51 51: 9 out of 9 lines of specbond.dat converted successfully 51: Special Atom Distance matrix: 51: CYS25 HIS31 HIS51 51: SG14 NE264 NE2226 51: HIS31 NE264 1.921 51: HIS51 NE2226 1.498 2.650 51: CYS80 SG477 0.207 1.984 1.570 51: Linking CYS-25 SG-14 and CYS-80 SG-477... 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: 51: WARNING: Duplicate line found in or between hackblock and rtp entries 51: 51: Marked 150 virtual sites 51: Added 10 dummy masses 51: Added 29 new constraints 51: 51: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom H used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: 51: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 51: to an entry in the topology database, but the atom O used in 51: an interaction of type angle in that entry is not found in the 51: input file. Perhaps your atom and/or residue naming needs to be 51: fixed. 51: 51: 51: Before cleaning: 972 pairs 51: Before cleaning: 1270 dihedrals 51: Using the Gromos53a6 force field in directory gromos53a6.ff 51: 51: going to rename gromos53a6.ff/aminoacids.r2b 51: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 51: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 51: 51: Analyzing pdb file 51: Splitting chemical chains based on TER records or chain id changing. 51: 51: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 51: 51: chain #res #atoms 51: 51: 1 'A' 58 488 51: 51: All occupancies are one 51: 51: Reading residue database... (Gromos53a6) 51: 51: Using default: not generating all possible dihedrals 51: 51: Using default: excluding 3 bonded neighbors 51: 51: Using default: generating 1,4 H--H interactions 51: 51: Using default: removing proper dihedrals found on the same bond as a proper dihedral 51: 51: Processing chain 1 'A' (488 atoms, 58 residues) 51: 51: Identified residue ASN24 as a starting terminus. 51: 51: Identified residue ARG81 as a ending terminus. 51: Start terminus ASN-24: NH3+ 51: End terminus ARG-81: COO- 51: 51: Checking for duplicate atoms.... 51: 51: Generating any missing hydrogen atoms and/or adding termini. 51: 51: Now there are 58 residues with 639 atoms 51: 51: Making bonds... 51: 51: Number of bonds was 659, now 654 51: 51: Generating angles, dihedrals and pairs... 51: 51: Making cmap torsions... 51: 51: There are 321 dihedrals, 354 impropers, 963 angles 51: 972 pairs, 654 bonds and 141 virtual sites 51: 51: Total mass 6908.582 a.m.u. 51: 51: Total charge -6.000 e 51: 51: Writing topology 51: 51: Writing coordinate file... 51: 51: --------- PLEASE NOTE ------------ 51: 51: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 51: 51: The Gromos53a6 force field and the spce water model are used. 51: 51: --------- ETON ESAELP ------------ 51: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (237 ms) 51: [----------] 20 tests from G53a6/Pdb2gmxTest (2376 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 40 tests from 2 test suites ran. (4434 ms total) 51: [ PASSED ] 40 tests. 51/87 Test #51: Pdb2gmx2Test .............................. Passed 4.48 sec test 52 Start 52: Pdb2gmx3Test 52: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 39 tests from 6 test suites. 52: [----------] Global test environment set-up. 52: [----------] 10 tests from Amber/Pdb2gmxTest 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 653 pairs 52: Before cleaning: 691 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 255, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 691 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.132 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (139 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 748 pairs 52: Before cleaning: 788 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 291, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 788 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.366 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (132 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 676 pairs 52: Before cleaning: 727 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 262, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 727 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.124 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (102 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 603 pairs 52: Before cleaning: 634 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 233, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 634 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.888 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (77 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Before cleaning: 2499 pairs 52: Before cleaning: 2631 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 952, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2631 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.576 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (264 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 691 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 255, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 691 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.132 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (139 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 788 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 291, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 788 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.366 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (165 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 727 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 262, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 727 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.124 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (119 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 634 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 233, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 634 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.888 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (85 ms) 52: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2631 dihedrals 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 952, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2631 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.576 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Amber99sb-ildn force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (337 ms) 52: [----------] 10 tests from Amber/Pdb2gmxTest (1580 ms total) 52: 52: [----------] 1 test from AmberTip4p/Pdb2gmxTest 52: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 52: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 52: 52: going to rename amber99sb-ildn.ff/aminoacids.r2b 52: 52: going to rename amber99sb-ildn.ff/dna.r2b 52: 52: going to rename amber99sb-ildn.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 52: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 2 4 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Amber99sb-ildn) 52: 52: Processing chain 1 (4 atoms, 2 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 2 residues with 8 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 4, now 4 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 2 angles 52: 0 pairs, 4 bonds and 0 virtual sites 52: 52: Total mass 36.032 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 52: 52: The Amber99sb-ildn force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (66 ms) 52: [----------] 1 test from AmberTip4p/Pdb2gmxTest (66 ms total) 52: 52: [----------] 12 tests from Charmm/Pdb2gmxTest 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 663 dihedrals, 48 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.115 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (116 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 778 dihedrals, 49 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.361 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (113 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 696 dihedrals, 39 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.130 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (104 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 618 dihedrals, 38 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.885 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (83 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 56 cmap torsion pairs 52: 52: There are 2524 dihedrals, 149 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.566 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (126 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 39 pairs 52: Before cleaning: 39 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 52: Read 'GLU', 9 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 52: 52: chain #res #atoms 52: 52: 1 'X' 1 9 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'X' (9 atoms, 1 residues) 52: 52: Identified residue GLU1 as a starting terminus. 52: 52: Identified residue GLU1 as a ending terminus. 52: Start terminus GLU-1: NH3+ 52: End terminus GLU-1: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 1 residues with 18 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 17, now 17 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 39 dihedrals, 2 impropers, 30 angles 52: 39 pairs, 17 bonds and 0 virtual sites 52: 52: Total mass 146.123 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (30 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 663 dihedrals, 48 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.115 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (54 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 778 dihedrals, 49 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.361 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (87 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 696 dihedrals, 39 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.130 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (110 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 14 cmap torsion pairs 52: 52: There are 618 dihedrals, 38 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.885 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (92 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 56 cmap torsion pairs 52: 52: There are 2524 dihedrals, 149 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.566 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (256 ms) 52: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Marked 8 virtual sites 52: Added 2 dummy masses 52: Added 3 new constraints 52: Before cleaning: 39 pairs 52: Before cleaning: 39 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 52: Read 'GLU', 9 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 52: 52: chain #res #atoms 52: 52: 1 'X' 1 9 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'X' (9 atoms, 1 residues) 52: 52: Identified residue GLU1 as a starting terminus. 52: 52: Identified residue GLU1 as a ending terminus. 52: Start terminus GLU-1: NH3+ 52: End terminus GLU-1: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 1 residues with 18 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 17, now 17 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 39 dihedrals, 2 impropers, 30 angles 52: 39 pairs, 17 bonds and 9 virtual sites 52: 52: Total mass 146.123 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (54 ms) 52: [----------] 12 tests from Charmm/Pdb2gmxTest (1271 ms total) 52: 52: [----------] 8 tests from ChainSep/Pdb2gmxTest 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 651 pairs 52: Before cleaning: 661 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: Start terminus PHE-6: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 258 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 258, now 258 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 10 cmap torsion pairs 52: 52: There are 661 dihedrals, 46 impropers, 463 angles 52: 648 pairs, 258 bonds and 0 virtual sites 52: 52: Total mass 1882.146 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (92 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 123 pairs 52: Before cleaning: 123 dihedrals 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 10 donors and 7 acceptors were found. 52: There are 7 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS8 52: NE223 52: MET12 SD55 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 317 pairs 52: Before cleaning: 322 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 4 28 52: 52: 2 'B' 7 58 52: 52: 3 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (28 atoms, 4 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 51 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 50, now 50 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 123 dihedrals, 9 impropers, 88 angles 52: 123 pairs, 50 bonds and 0 virtual sites 52: 52: Total mass 434.421 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (58 atoms, 7 residues) 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus PHE-6: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 7 residues with 124 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 125, now 125 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 5 cmap torsion pairs 52: 52: There are 322 dihedrals, 19 impropers, 227 angles 52: 314 pairs, 125 bonds and 0 virtual sites 52: 52: Total mass 846.083 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 51 atoms 4 residues 52: 52: Including chain 2 in system: 124 atoms 7 residues 52: 52: Including chain 3 in system: 83 atoms 5 residues 52: 52: Now there are 258 atoms and 16 residues 52: 52: Total mass in system 1882.146 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (89 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 651 pairs 52: Before cleaning: 661 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ILE-9: COO- 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 258 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 258, now 258 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 10 cmap torsion pairs 52: 52: There are 661 dihedrals, 46 impropers, 463 angles 52: 648 pairs, 258 bonds and 0 virtual sites 52: 52: Total mass 1882.146 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (92 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 10 donors and 12 acceptors were found. 52: There are 13 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 52: SG9 52: HIS8 NE251 1.055 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 288 pairs 52: Before cleaning: 293 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 152 pairs 52: Before cleaning: 152 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 8 61 52: 52: 2 'B' 3 25 52: 52: 3 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (61 atoms, 8 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ILE-9: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 8 residues with 114 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 115, now 115 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6 cmap torsion pairs 52: 52: There are 293 dihedrals, 23 impropers, 203 angles 52: 285 pairs, 115 bonds and 0 virtual sites 52: 52: Total mass 888.952 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (25 atoms, 3 residues) 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 61 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 60, now 60 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 152 dihedrals, 5 impropers, 112 angles 52: 152 pairs, 60 bonds and 0 virtual sites 52: 52: Total mass 391.552 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 114 atoms 8 residues 52: 52: Including chain 2 in system: 61 atoms 3 residues 52: 52: Including chain 3 in system: 83 atoms 5 residues 52: 52: Now there are 258 atoms and 16 residues 52: 52: Total mass in system 1882.146 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (77 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 650 pairs 52: Before cleaning: 660 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Merged chains into joint molecule definitions at 3 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: Start terminus PHE-6: NH3+ 52: End terminus ILE-9: COO- 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 261 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 260, now 260 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 8 cmap torsion pairs 52: 52: There are 660 dihedrals, 45 impropers, 466 angles 52: 647 pairs, 260 bonds and 0 virtual sites 52: 52: Total mass 1900.162 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (92 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 123 pairs 52: Before cleaning: 123 dihedrals 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 6 donors and 4 acceptors were found. 52: There are 3 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 164 pairs 52: Before cleaning: 169 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 152 pairs 52: Before cleaning: 152 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 4 28 52: 52: 2 'B' 4 33 52: 52: 3 'B' 3 25 52: 52: 4 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (28 atoms, 4 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue GLU5 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus GLU-5: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 51 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 50, now 50 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 123 dihedrals, 9 impropers, 88 angles 52: 123 pairs, 50 bonds and 0 virtual sites 52: 52: Total mass 434.421 a.m.u. 52: 52: Total charge -2.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (33 atoms, 4 residues) 52: 52: Identified residue PHE6 as a starting terminus. 52: 52: Identified residue ILE9 as a ending terminus. 52: Start terminus PHE-6: NH3+ 52: End terminus ILE-9: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 4 residues with 66 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 67, now 67 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2 cmap torsion pairs 52: 52: There are 169 dihedrals, 13 impropers, 118 angles 52: 161 pairs, 67 bonds and 0 virtual sites 52: 52: Total mass 472.547 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'B' (25 atoms, 3 residues) 52: 52: Identified residue LYS10 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus LYS-10: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 61 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 60, now 60 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 152 dihedrals, 5 impropers, 112 angles 52: 152 pairs, 60 bonds and 0 virtual sites 52: 52: Total mass 391.552 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Processing chain 4 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 51 atoms 4 residues 52: 52: Including chain 2 in system: 66 atoms 4 residues 52: 52: Including chain 3 in system: 61 atoms 3 residues 52: 52: Including chain 4 in system: 83 atoms 5 residues 52: 52: Now there are 261 atoms and 16 residues 52: 52: Total mass in system 1900.162 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (90 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 652 pairs 52: Before cleaning: 662 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: Merged chains into joint molecule definitions at 1 places. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 16 127 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (127 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus MET-12: COO- 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 256, now 256 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 12 cmap torsion pairs 52: 52: There are 662 dihedrals, 47 impropers, 460 angles 52: 649 pairs, 256 bonds and 0 virtual sites 52: 52: Total mass 1864.131 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (96 ms) 52: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 14 donors and 15 acceptors were found. 52: There are 20 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 441 pairs 52: Before cleaning: 446 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 211 pairs 52: Before cleaning: 216 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 11 86 52: 52: 2 'C' 5 41 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (86 atoms, 11 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue MET12 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus MET-12: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 11 residues with 172 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 173, now 173 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 9 cmap torsion pairs 52: 52: There are 446 dihedrals, 29 impropers, 312 angles 52: 438 pairs, 173 bonds and 0 virtual sites 52: 52: Total mass 1262.488 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'C' (41 atoms, 5 residues) 52: 52: Identified residue ASN13 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ASN-13: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 5 residues with 83 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 83, now 83 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 3 cmap torsion pairs 52: 52: There are 216 dihedrals, 18 impropers, 148 angles 52: 211 pairs, 83 bonds and 0 virtual sites 52: 52: Total mass 601.643 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 172 atoms 11 residues 52: 52: Including chain 2 in system: 83 atoms 5 residues 52: 52: Now there are 255 atoms and 16 residues 52: 52: Total mass in system 1864.131 a.m.u. 52: 52: Total charge in system 0.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (89 ms) 52: [----------] 8 tests from ChainSep/Pdb2gmxTest (723 ms total) 52: 52: [----------] 4 tests from ChainChanges/Pdb2gmxTest 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on changing chain id only (ignoring TER records). 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (64 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records only (ignoring chain id). 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (76 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (68 ms) 52: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 83 pairs 52: Before cleaning: 83 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 145 pairs 52: Before cleaning: 150 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 52: Read 'Fragments of peptides and ions', 47 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records and chain id changing. 52: 52: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 3 19 52: 52: 2 'B' 3 28 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (19 atoms, 3 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue ASP4 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus ASP-4: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 36 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 35, now 35 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 83 dihedrals, 6 impropers, 61 angles 52: 83 pairs, 35 bonds and 0 virtual sites 52: 52: Total mass 306.314 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'B' (28 atoms, 3 residues) 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue TRP20 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus TRP-20: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 3 residues with 57 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 58, now 58 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 1 cmap torsion pairs 52: 52: There are 150 dihedrals, 5 impropers, 103 angles 52: 142 pairs, 58 bonds and 0 virtual sites 52: 52: Total mass 404.468 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Writing topology 52: 52: Including chain 1 in system: 36 atoms 3 residues 52: 52: Including chain 2 in system: 57 atoms 3 residues 52: 52: Now there are 93 atoms and 6 residues 52: 52: Total mass in system 710.782 a.m.u. 52: 52: Total charge in system -1.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (72 ms) 52: [----------] 4 tests from ChainChanges/Pdb2gmxTest (283 ms total) 52: 52: [----------] 4 tests from Cyclic/Pdb2gmxTest 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: WARNING: all CONECT records are ignored 52: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 6040 pairs 52: Before cleaning: 6605 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 6040 pairs 52: Before cleaning: 6605 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 52: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 52: 52: Moved all the water blocks to the end 52: 52: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 52: 52: chain #res #atoms 52: 52: 1 'P' 71 1527 52: 52: 2 'Q' 71 1527 52: 52: 3 'Q' 7 7 52: 52: 4 ' ' 10 10 (only water) 52: 52: 5 ' ' 16 16 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'P' (1527 atoms, 71 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 71 residues with 2297 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 2481, now 2481 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6605 dihedrals, 183 impropers, 4434 angles 52: 5827 pairs, 2481 bonds and 0 virtual sites 52: 52: Total mass 22984.514 a.m.u. 52: 52: Total charge -71.000 e 52: 52: Writing topology 52: 52: Processing chain 2 'Q' (1527 atoms, 71 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 71 residues with 2297 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: Number of bonds was 2481, now 2481 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 6605 dihedrals, 183 impropers, 4434 angles 52: 5827 pairs, 2481 bonds and 0 virtual sites 52: 52: Total mass 22984.514 a.m.u. 52: 52: Total charge -71.000 e 52: 52: Writing topology 52: 52: Processing chain 3 'Q' (7 atoms, 7 residues) 52: 52: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 52: 52: Disabling further notes about ions. 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 7 residues with 7 atoms 52: Chain time... 52: 52: Making bonds... 52: 52: No bonds 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 0 angles 52: 0 pairs, 0 bonds and 0 virtual sites 52: 52: Total mass 170.135 a.m.u. 52: 52: Total charge 14.000 e 52: 52: Writing topology 52: 52: Processing chain 4 (10 atoms, 10 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 10 residues with 30 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 30, now 30 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 30 angles 52: 0 pairs, 30 bonds and 0 virtual sites 52: 52: Total mass 180.154 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Processing chain 5 (16 atoms, 16 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 48 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 48, now 48 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 48 angles 52: 0 pairs, 48 bonds and 0 virtual sites 52: 52: Total mass 288.246 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Including chain 1 in system: 2297 atoms 71 residues 52: 52: Including chain 2 in system: 2297 atoms 71 residues 52: 52: Including chain 3 in system: 7 atoms 7 residues 52: 52: Including chain 4 in system: 30 atoms 10 residues 52: 52: Including chain 5 in system: 48 atoms 16 residues 52: 52: Now there are 4679 atoms and 175 residues 52: 52: Total mass in system 46607.563 a.m.u. 52: 52: Total charge in system -128.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (1122 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2325 pairs 52: Before cleaning: 2325 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 52: Read 'CARNOCYCLIN-A', 413 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 60 413 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (413 atoms, 60 residues) 52: 52: Identified residue LEU1 as a starting terminus. 52: 52: Identified residue LEU60 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 60 residues with 878 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 880, now 880 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 60 cmap torsion pairs 52: 52: There are 2325 dihedrals, 137 impropers, 1614 angles 52: 2319 pairs, 880 bonds and 0 virtual sites 52: 52: Total mass 5866.087 a.m.u. 52: 52: Total charge 4.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (219 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: WARNING: all CONECT records are ignored 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 12080 pairs 52: Before cleaning: 13210 dihedrals 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 52: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: Moved all the water blocks to the end 52: 52: Merged chains into joint molecule definitions at 2 places. 52: 52: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 52: 52: chain #res #atoms 52: 52: 1 'P' 149 3061 52: 52: 2 ' ' 10 10 (only water) 52: 52: 3 ' ' 16 16 (only water) 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'P' (3061 atoms, 149 residues) 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Identified residue G1 as a starting terminus. 52: 52: Identified residue U71 as a ending terminus. 52: 52: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 52: 52: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 52: 52: Disabling further notes about ions. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 149 residues with 4601 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 4962, now 4962 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 13210 dihedrals, 366 impropers, 8868 angles 52: 11654 pairs, 4962 bonds and 0 virtual sites 52: 52: Total mass 46139.162 a.m.u. 52: 52: Total charge -128.000 e 52: 52: Writing topology 52: 52: Processing chain 2 (10 atoms, 10 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 10 residues with 30 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 30, now 30 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 30 angles 52: 0 pairs, 30 bonds and 0 virtual sites 52: 52: Total mass 180.154 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Processing chain 3 (16 atoms, 16 residues) 52: 52: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 48 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 48, now 48 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 0 dihedrals, 0 impropers, 48 angles 52: 0 pairs, 48 bonds and 0 virtual sites 52: 52: Total mass 288.246 a.m.u. 52: 52: Total charge 0.000 e 52: 52: Including chain 1 in system: 4601 atoms 149 residues 52: 52: Including chain 2 in system: 30 atoms 10 residues 52: 52: Including chain 3 in system: 48 atoms 16 residues 52: 52: Now there are 4679 atoms and 175 residues 52: 52: Total mass in system 46607.563 a.m.u. 52: 52: Total charge in system -128.000 e 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (1425 ms) 52: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 52: 9 out of 9 lines of specbond.dat converted successfully 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 52: Before cleaning: 2325 pairs 52: Before cleaning: 2325 dihedrals 52: Using the Charmm27 force field in directory charmm27.ff 52: 52: going to rename charmm27.ff/aminoacids.r2b 52: 52: going to rename charmm27.ff/rna.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 52: Read 'CARNOCYCLIN-A', 413 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 60 413 52: 52: All occupancies are one 52: 52: Reading residue database... (Charmm27) 52: 52: Processing chain 1 'A' (413 atoms, 60 residues) 52: 52: Identified residue LEU1 as a starting terminus. 52: 52: Identified residue LEU60 as a ending terminus. 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 60 residues with 878 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 880, now 880 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 60 cmap torsion pairs 52: 52: There are 2325 dihedrals, 137 impropers, 1614 angles 52: 2319 pairs, 880 bonds and 0 virtual sites 52: 52: Total mass 5866.087 a.m.u. 52: 52: Total charge 4.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 52: 52: The Charmm27 force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (153 ms) 52: [----------] 4 tests from Cyclic/Pdb2gmxTest (2956 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 39 tests from 6 test suites ran. (6881 ms total) 52: [ PASSED ] 39 tests. 52/87 Test #52: Pdb2gmx3Test .............................. Passed 6.95 sec test 53 Start 53: CorrelationsTest 53: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 53: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/correlationfunctions/tests 53: Test timeout computed to be: 30 53: [==========] Running 21 tests from 3 test suites. 53: [----------] Global test environment set-up. 53: [----------] 10 tests from AutocorrTest 53: [ RUN ] AutocorrTest.EacNormal 53: [ OK ] AutocorrTest.EacNormal (67 ms) 53: [ RUN ] AutocorrTest.EacNoNormalize 53: [ OK ] AutocorrTest.EacNoNormalize (25 ms) 53: [ RUN ] AutocorrTest.EacCos 53: [ OK ] AutocorrTest.EacCos (60 ms) 53: [ RUN ] AutocorrTest.EacVector 53: [ OK ] AutocorrTest.EacVector (70 ms) 53: [ RUN ] AutocorrTest.EacRcross 53: [ OK ] AutocorrTest.EacRcross (0 ms) 53: [ RUN ] AutocorrTest.EacP0 53: [ OK ] AutocorrTest.EacP0 (42 ms) 53: [ RUN ] AutocorrTest.EacP1 53: [ OK ] AutocorrTest.EacP1 (37 ms) 53: [ RUN ] AutocorrTest.EacP2 53: [ OK ] AutocorrTest.EacP2 (70 ms) 53: [ RUN ] AutocorrTest.EacP3 53: [ OK ] AutocorrTest.EacP3 (1 ms) 53: [ RUN ] AutocorrTest.EacP4 53: [ OK ] AutocorrTest.EacP4 (26 ms) 53: [----------] 10 tests from AutocorrTest (403 ms total) 53: 53: [----------] 10 tests from ExpfitTest 53: [ RUN ] ExpfitTest.EffnEXP1 53: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 53: [ RUN ] ExpfitTest.EffnEXP2 53: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 53: [ RUN ] ExpfitTest.EffnEXPEXP 53: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 53: [ RUN ] ExpfitTest.EffnEXP5 53: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 53: [ RUN ] ExpfitTest.EffnEXP7 53: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 53: [ RUN ] ExpfitTest.EffnEXP9 53: [ OK ] ExpfitTest.EffnEXP9 (17 ms) 53: [ RUN ] ExpfitTest.EffnERF 53: [ OK ] ExpfitTest.EffnERF (9 ms) 53: [ RUN ] ExpfitTest.EffnERREST 53: [ OK ] ExpfitTest.EffnERREST (1 ms) 53: [ RUN ] ExpfitTest.EffnVAC 53: [ OK ] ExpfitTest.EffnVAC (15 ms) 53: [ RUN ] ExpfitTest.EffnPRES 53: [ OK ] ExpfitTest.EffnPRES (18 ms) 53: [----------] 10 tests from ExpfitTest (85 ms total) 53: 53: [----------] 1 test from ManyAutocorrelationTest 53: [ RUN ] ManyAutocorrelationTest.Empty 53: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 53: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 21 tests from 3 test suites ran. (506 ms total) 53: [ PASSED ] 21 tests. 53/87 Test #53: CorrelationsTest .......................... Passed 0.58 sec test 54 Start 54: AnalysisDataUnitTests 54: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 54: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/analysisdata/tests 54: Test timeout computed to be: 30 54: [==========] Running 69 tests from 14 test suites. 54: [----------] Global test environment set-up. 54: [----------] 3 tests from AnalysisDataInitializationTest 54: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 54: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 54: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 54: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 54: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 54: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 54: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 54: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (13 ms) 54: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/0 (14 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 54: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 54: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 54: 54: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 54: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 54: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 54: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 54: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 54: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 54: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 54: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 54: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 54: 54: [----------] 4 tests from AnalysisArrayDataTest 54: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 54: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 54: [ RUN ] AnalysisArrayDataTest.StorageWorks 54: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 54: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 54: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 54: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 54: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 54: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 54: 54: [----------] 6 tests from AverageModuleTest 54: [ RUN ] AverageModuleTest.BasicTest 54: [ OK ] AverageModuleTest.BasicTest (0 ms) 54: [ RUN ] AverageModuleTest.HandlesMultipointData 54: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 54: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 54: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 54: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 54: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 54: [ RUN ] AverageModuleTest.CanCustomizeXAxis 54: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 54: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 54: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 54: [----------] 6 tests from AverageModuleTest (1 ms total) 54: 54: [----------] 2 tests from FrameAverageModuleTest 54: [ RUN ] FrameAverageModuleTest.BasicTest 54: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 54: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 54: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 54: 54: [----------] 7 tests from AnalysisHistogramSettingsTest 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 54: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 54: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 54: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 54: 54: [----------] 2 tests from SimpleHistogramModuleTest 54: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 54: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (16 ms) 54: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 54: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [----------] 2 tests from SimpleHistogramModuleTest (17 ms total) 54: 54: [----------] 3 tests from WeightedHistogramModuleTest 54: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 54: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 54: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 54: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 54: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 54: 54: [----------] 3 tests from BinAverageModuleTest 54: [ RUN ] BinAverageModuleTest.ComputesCorrectly 54: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 54: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 54: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 54: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 54: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 3 tests from BinAverageModuleTest (0 ms total) 54: 54: [----------] 4 tests from AbstractAverageHistogramTest 54: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 54: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 54: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 54: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 54: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 54: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (12 ms) 54: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 54: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 54: [----------] 4 tests from AbstractAverageHistogramTest (14 ms total) 54: 54: [----------] 3 tests from LifetimeModuleTest 54: [ RUN ] LifetimeModuleTest.BasicTest 54: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 54: [ RUN ] LifetimeModuleTest.CumulativeTest 54: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 54: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 54: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 54: [----------] 3 tests from LifetimeModuleTest (0 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 69 tests from 14 test suites ran. (55 ms total) 54: [ PASSED ] 69 tests. 54/87 Test #54: AnalysisDataUnitTests ..................... Passed 0.12 sec test 55 Start 55: CoordinateIOTests 55: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml" 55: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/coordinateio/tests 55: Test timeout computed to be: 30 55: [==========] Running 67 tests from 20 test suites. 55: [----------] Global test environment set-up. 55: [----------] 1 test from OutputSelectorDeathTest 55: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (41 ms) 55: [----------] 1 test from OutputSelectorDeathTest (41 ms total) 55: 55: [----------] 5 tests from TrajectoryFrameWriterTest 55: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 55: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (13 ms) 55: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 55: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 55: [----------] 5 tests from TrajectoryFrameWriterTest (16 ms total) 55: 55: [----------] 5 tests from OutputAdapterContainer 55: [ RUN ] OutputAdapterContainer.MakeEmpty 55: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 55: [ RUN ] OutputAdapterContainer.AddAdapter 55: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.RejectBadAdapter 55: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 55: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 55: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 55: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 55: [----------] 5 tests from OutputAdapterContainer (0 ms total) 55: 55: [----------] 3 tests from RegisterFrameConverterTest 55: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 55: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 55: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 55: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 55: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 55: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 55: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 55: 55: [----------] 5 tests from FlagTest 55: [ RUN ] FlagTest.CanSetSimpleFlag 55: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 55: [ RUN ] FlagTest.CanAddNewBox 55: [ OK ] FlagTest.CanAddNewBox (0 ms) 55: [ RUN ] FlagTest.SetsImplicitPrecisionChange 55: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 55: [ RUN ] FlagTest.SetsImplicitStartTimeChange 55: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 55: [ RUN ] FlagTest.SetsImplicitTimeStepChange 55: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 55: [----------] 5 tests from FlagTest (0 ms total) 55: 55: [----------] 5 tests from SetAtomsTest 55: [ RUN ] SetAtomsTest.RemovesExistingAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 55: [ RUN ] SetAtomsTest.AddsNewAtoms 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 55: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (0 ms) 55: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 55: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 55: [----------] 5 tests from SetAtomsTest (16 ms total) 55: 55: [----------] 2 tests from SetBothTimeTest 55: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 55: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 55: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 55: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 55: [----------] 2 tests from SetBothTimeTest (0 ms total) 55: 55: [----------] 2 tests from SetStartTimeTest 55: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 55: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 55: [ RUN ] SetStartTimeTest.WorksWithZeroStart 55: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 55: [----------] 2 tests from SetStartTimeTest (0 ms total) 55: 55: [----------] 1 test from SetTimeStepTest 55: [ RUN ] SetTimeStepTest.SetTimeStepWorks 55: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 55: [----------] 1 test from SetTimeStepTest (0 ms total) 55: 55: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (12 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 55: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (0 ms) 55: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (17 ms total) 55: 55: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (17 ms) 55: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (18 ms total) 55: 55: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 55: 55: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (1 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (18 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (1 ms) 55: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (14 ms) 55: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (35 ms total) 55: 55: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (12 ms) 55: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (14 ms total) 55: 55: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 55: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 55: 55: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 55: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 55: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 55: 55: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 55: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 55: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 55: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 55: 55: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 55: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (20 ms) 55: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (21 ms total) 55: 55: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 55: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 55: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 55: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 55: 55: [----------] 4 tests from ModuleSupported/NoOptionalOutput 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (0 ms) 55: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 55: 55: WARNING: Masses and atomic (Van der Waals) radii will be guessed 55: based on residue and atom names, since they could not be 55: definitively assigned from the information in your input 55: files. These guessed numbers might deviate from the mass 55: and radius of the atom type. Please check the output 55: files if necessary. Note, that this functionality may 55: be removed in a future GROMACS version. Please, consider 55: using another file format for your input. 55: 55: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 55: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 67 tests from 20 test suites ran. (189 ms total) 55: [ PASSED ] 67 tests. 55/87 Test #55: CoordinateIOTests ......................... Passed 0.27 sec test 56 Start 56: TrajectoryAnalysisUnitTests 56: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests 56: Test timeout computed to be: 1920 56: [==========] Running 385 tests from 24 test suites. 56: [----------] Global test environment set-up. 56: [----------] 11 tests from AngleModuleTest 56: [ RUN ] AngleModuleTest.ComputesSimpleAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesSimpleAngles (2 ms) 56: [ RUN ] AngleModuleTest.ComputesDihedrals 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesDihedrals (9 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (13 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 56: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 56: Reading frames from gro file 'Test system for different angles', 33 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (13 ms) 56: [ RUN ] AngleModuleTest.ComputesMultipleAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.ComputesMultipleAngles (1 ms) 56: [ RUN ] AngleModuleTest.HandlesDynamicSelections 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 56: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (9 ms) 56: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (1 ms) 56: [----------] 11 tests from AngleModuleTest (56 ms total) 56: 56: [----------] 5 tests from ClustsizeTest 56: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 56: There is one group in the index 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 24 56: cmid: 2, cmax: 4, max_size: 6 56: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 56: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (0 ms) 56: [ RUN ] ClustsizeTest.NoMolShortCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 56: There is one group in the index 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 24 56: cmid: 1, cmax: 6, max_size: 6 56: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 56: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (0 ms) 56: [ RUN ] ClustsizeTest.MolDefaultCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 2, cmax: 4, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (13 ms) 56: [ RUN ] ClustsizeTest.MolShortCutoff 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 1, cmax: 6, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 56: [ RUN ] ClustsizeTest.MolCSize 56: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Total number of atoms in clusters = 8 56: cmid: 2, cmax: 4, max_size: 2 56: 50%100%cmid: 2, cmax: 6, max_size: 2 56: 50%100%[ OK ] ClustsizeTest.MolCSize (0 ms) 56: [----------] 5 tests from ClustsizeTest (16 ms total) 56: 56: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 56: Reading frames from gro file 'Test system', 8 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (17 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 56: Reading frames from gro file 'Test system', 8 atoms. 56: Reading frame 0 time 0.000 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (1 ms) 56: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 56: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 56: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (19 ms total) 56: 56: [----------] 4 tests from ConvertTrjModuleTest 56: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (21 ms) 56: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (37 ms) 56: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (1 ms) 56: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 56: Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (0 ms) 56: [----------] 4 tests from ConvertTrjModuleTest (61 ms total) 56: 56: [----------] 6 tests from DistanceModuleTest 56: [ RUN ] DistanceModuleTest.ComputesDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2: 56: Number of samples: 5 56: Average distance: 1.43246 nm 56: Standard deviation: 0.96700 nm 56: [ OK ] DistanceModuleTest.ComputesDistances (21 ms) 56: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2: 56: Number of samples: 5 56: Average distance: 1.43246 nm 56: Standard deviation: 0.96700 nm 56: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 56: Number of samples: 4 56: Average distance: 1.81066 nm 56: Standard deviation: 0.79289 nm 56: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) 56: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: atomname S1 S2 and res_cog x < 2.8: 56: Number of samples: 3 56: Average distance: 1.72076 nm 56: Standard deviation: 1.24839 nm 56: [ OK ] DistanceModuleTest.HandlesDynamicSelections (17 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: Contacts: 56: Number of samples: 2 56: Average distance: 1.00000 nm 56: Standard deviation: 0.00000 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (19 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: SuccessiveContacts: 56: Number of samples: 2 56: Average distance: 1.00000 nm 56: Standard deviation: 0.00000 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (23 ms) 56: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: ManyContacts: 56: Number of samples: 10 56: Average distance: 1.82913 nm 56: Standard deviation: 0.78478 nm 56: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (19 ms) 56: [----------] 6 tests from DistanceModuleTest (105 ms total) 56: 56: [----------] 2 tests from ExtractClusterModuleTest 56: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 56: trr version: GMX_trn_file (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 56: Analyzed 26 frames, last time 0.050 56: There are 8 clusters containing 26 structures, highest framenr is 25 56: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (1 ms) 56: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 56: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 56: Analyzed 26 frames, last time 0.050 56: There are 8 clusters containing 26 structures, highest framenr is 25 56: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (17 ms) 56: [----------] 2 tests from ExtractClusterModuleTest (18 ms total) 56: 56: [----------] 2 tests from FreeVolumeModuleTest 56: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for CO2-RM. Set to zero. 56: Could not determine VDW radius for 40 particles. These were set to zero. 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: cutoff = 0.18 nm 56: probe_radius = 0 nm 56: seed = 13 56: ninsert = 1000 probes per nm^3 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 56: van der Spoel and Luciano T. Costa 56: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 56: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 56: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Free volume 38.02 +/- 0.00 % 56: Total volume 68.92 +/- 0.00 nm^3 56: Number of molecules 340 total mass 63491.38 Dalton 56: Average molar mass: 186.74 Dalton 56: Density rho: 1529.71 +/- 0.00 nm^3 56: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 56: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 56: Fractional free volume 0.194 +/- 0.000 56: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (235 ms) 56: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: cutoff = 0.18 nm 56: probe_radius = 0 nm 56: seed = 17 56: ninsert = 1000 probes per nm^3 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 56: van der Spoel and Luciano T. Costa 56: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 56: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 56: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Free volume 38.48 +/- 0.00 % 56: Total volume 68.92 +/- 0.00 nm^3 56: Number of molecules 340 total mass 63491.38 Dalton 56: Average molar mass: 186.74 Dalton 56: Density rho: 1529.71 +/- 0.00 nm^3 56: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 56: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 56: Fractional free volume 0.200 +/- 0.000 56: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (276 ms) 56: [----------] 2 tests from FreeVolumeModuleTest (512 ms total) 56: 56: [----------] 11 tests from MsdModuleTest 56: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.threeDimensionalDiffusion (1 ms) 56: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 56: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.oneDimensionalDiffusion (49 ms) 56: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 56: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 56: Analyzed 10 frames, last time 9.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 56: [ RUN ] MsdModuleTest.roundingFail 56: Reading frame 0 time 0.000 Reading frame 1 time 0.001 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] MsdModuleTest.roundingFail (0 ms) 56: [ RUN ] MsdModuleTest.multipleGroupsWork 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to 1911553887 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.multipleGroupsWork (111 ms) 56: [ DISABLED ] MsdModuleTest.DISABLED_trestartLessThanDt 56: [ RUN ] MsdModuleTest.trestartGreaterThanDt 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -579686425 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.trestartGreaterThanDt (71 ms) 56: [ RUN ] MsdModuleTest.molTest 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -369758529 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.molTest (74 ms) 56: [ RUN ] MsdModuleTest.beginFit 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -220301377 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.beginFit (46 ms) 56: [ RUN ] MsdModuleTest.endFit 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -471879745 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.endFit (54 ms) 56: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 56: For energy conservation with LINCS, lincs_iter should be 2 or larger. 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 1818.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: NVE simulation: will use the initial temperature of 288.764 K for 56: determining the Verlet buffer size 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: There are 9 non-linear virtual site constructions. Their contribution to 56: the energy error is approximated. In most cases this does not affect the 56: error significantly. 56: 56: 56: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 5 NOTEs 56: NOTE: You provided an index file 56: /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 56: (with -n), but it was not used by any selection. 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 2.000 56: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 56: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 56: Analyzed 21 frames, last time 40.000 56: Setting the LD random seed to -626541121 56: 56: Generated 2145 of the 2145 non-bonded parameter combinations 56: 56: Generated 2145 of the 2145 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 56: 56: Excluding 2 bonded neighbours molecule type 'SOL' 56: 56: Cleaning up constraints and constant bonded interactions with virtual sites 56: 56: Converted 15 Bonds with virtual sites to connections, 7 left 56: 56: Removed 18 Angles with virtual sites, 21 left 56: 56: Removed 10 Proper Dih.s with virtual sites, 44 left 56: 56: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 56: 56: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 56: 56: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 56: 56: Note that mdrun will redetermine rlist based on the actual pair-list setup 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (39 ms) 56: [----------] 11 tests from MsdModuleTest (452 ms total) 56: 56: [----------] 9 tests from PairDistanceModuleTest 56: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (9 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (1 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (9 ms) 56: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 56: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (1 ms) 56: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (3 ms) 56: [----------] 9 tests from PairDistanceModuleTest (30 ms total) 56: 56: [----------] 5 tests from RdfModuleTest 56: [ RUN ] RdfModuleTest.BasicTest 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.BasicTest (44 ms) 56: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 56: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 56: Reading frame 0 time 0.000 Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (67 ms) 56: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (68 ms) 56: [ RUN ] RdfModuleTest.CalculatesSurf 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.CalculatesSurf (49 ms) 56: [ RUN ] RdfModuleTest.CalculatesXY 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] RdfModuleTest.CalculatesXY (87 ms) 56: [----------] 5 tests from RdfModuleTest (317 ms total) 56: 56: [----------] 5 tests from SasaModuleTest 56: [ RUN ] SasaModuleTest.BasicTest 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.BasicTest (25 ms) 56: [ RUN ] SasaModuleTest.HandlesSelectedResidues 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesSelectedResidues (19 ms) 56: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (22 ms) 56: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (28 ms) 56: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 56: Michael Scharf 56: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 56: of Surface Area and Volume and to Dot Surface Contouring of Molecular 56: Assemblies 56: J. Comp. Chem. 16 (1995) pp. 273-284 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 56: from the source below. This means the results may be different 56: compared to previous GROMACS versions. 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. Bondi 56: van der Waals Volumes and Radii 56: J. Phys. Chem. 68 (1964) pp. 441-451 56: -------- -------- --- Thank You --- -------- -------- 56: 56: Analyzed topology coordinates 56: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (23 ms) 56: [----------] 5 tests from SasaModuleTest (120 ms total) 56: 56: [----------] 8 tests from SelectModuleTest 56: [ RUN ] SelectModuleTest.BasicTest 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.BasicTest (2 ms) 56: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (17 ms) 56: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (1 ms) 56: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (21 ms) 56: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (1 ms) 56: [ RUN ] SelectModuleTest.NormalizesSizes 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 56: [ RUN ] SelectModuleTest.WritesResidueNumbers 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.WritesResidueNumbers (21 ms) 56: [ RUN ] SelectModuleTest.WritesResidueIndices 56: Analyzed topology coordinates 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 56: [----------] 8 tests from SelectModuleTest (68 ms total) 56: 56: [----------] 10 tests from SurfaceAreaTest 56: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 56: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 56: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 56: [ OK ] SurfaceAreaTest.ComputesTwoPoints (0 ms) 56: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 56: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints12 56: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints32 56: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints42 56: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 56: [ RUN ] SurfaceAreaTest.SurfacePoints122 56: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 56: [ RUN ] SurfaceAreaTest.Computes100Points 56: [ OK ] SurfaceAreaTest.Computes100Points (20 ms) 56: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 56: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 56: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 56: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (1 ms) 56: [----------] 10 tests from SurfaceAreaTest (25 ms total) 56: 56: [----------] 4 tests from TopologyInformation 56: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 56: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 56: [ RUN ] TopologyInformation.WorksWithGroFile 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TopologyInformation.WorksWithGroFile (21 ms) 56: [ RUN ] TopologyInformation.WorksWithPdbFile 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 56: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 56: 56: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: For a correct single-point energy evaluation with nsteps = 0, use 56: continuation = yes to avoid constraining the input coordinates. 56: 56: Generating 1-4 interactions: fudge = 0.5 56: 56: NOTE 2 [file lysozyme.top, line 1465]: 56: System has non-zero total charge: 2.000000 56: Total charge should normally be an integer. See 56: https://manual.gromacs.org/current/user-guide/floating-point.html 56: for discussion on how close it should be to an integer. 56: 56: 56: 56: Number of degrees of freedom in T-Coupling group rest is 465.00 56: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 56: 56: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: NVE simulation with an initial temperature of zero: will use a Verlet 56: buffer of 10%. Check your energy drift! 56: 56: 56: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 56: You are using a plain Coulomb cut-off, which might produce artifacts. 56: You might want to consider using PME electrostatics. 56: 56: 56: 56: There were 4 NOTEs 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 56: Setting the LD random seed to 1006427763 56: 56: Generated 330891 of the 330891 non-bonded parameter combinations 56: 56: Generated 330891 of the 330891 1-4 parameter combinations 56: 56: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 56: Analysing residue names: 56: There are: 10 Protein residues 56: Analysing Protein... 56: 56: This run will generate roughly 0 Mb of data 56: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (1265 ms) 56: [----------] 4 tests from TopologyInformation (1287 ms total) 56: 56: [----------] 4 tests from TrajectoryModuleTest 56: [ RUN ] TrajectoryModuleTest.BasicTest 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.BasicTest (17 ms) 56: [ RUN ] TrajectoryModuleTest.PlotsXOnly 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 56: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (1 ms) 56: [ RUN ] TrajectoryModuleTest.HandlesNoForces 56: Reading frames from gro file 'Test system', 15 atoms. 56: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 56: Analyzed 2 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: [ OK ] TrajectoryModuleTest.HandlesNoForces (13 ms) 56: [----------] 4 tests from TrajectoryModuleTest (33 ms total) 56: 56: [----------] 5 tests from UnionFinderTest 56: [ RUN ] UnionFinderTest.WorksEmpty 56: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 56: [ RUN ] UnionFinderTest.BasicMerges 56: [ OK ] UnionFinderTest.BasicMerges (0 ms) 56: [ RUN ] UnionFinderTest.LargerMerges 56: [ OK ] UnionFinderTest.LargerMerges (0 ms) 56: [ RUN ] UnionFinderTest.LongRightMerge 56: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 56: [ RUN ] UnionFinderTest.LongLeftMerge 56: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 56: [----------] 5 tests from UnionFinderTest (0 ms total) 56: 56: [----------] 1 test from MappedUnionFinderTest 56: [ RUN ] MappedUnionFinderTest.BasicMerges 56: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 56: [----------] 1 test from MappedUnionFinderTest (0 ms total) 56: 56: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/0 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/0 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/1 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/1 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/2 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/2 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/3 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/3 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/4 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/4 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/5 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/5 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/6 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/6 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/7 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/7 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/8 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/8 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/9 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/9 (73 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/10 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/10 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/11 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/11 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/12 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/12 (74 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/13 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/13 (66 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/14 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/14 (57 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/15 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/15 (74 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/16 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/16 (72 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/17 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/17 (72 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/18 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/18 (72 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/19 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/19 (76 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/20 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/20 (73 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/21 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/21 (81 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/22 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/22 (76 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/23 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/23 (76 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/24 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/24 (101 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/25 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/25 (93 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/26 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/26 (101 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/27 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/27 (105 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/28 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/28 (106 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/29 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/29 (98 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/30 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/30 (106 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/31 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/31 (110 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/32 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/32 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/33 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/33 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/34 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/34 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/35 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/35 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/36 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/36 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/37 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/37 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/38 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/38 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/39 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/39 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/40 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/40 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/41 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/41 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/42 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/42 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/43 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/43 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/44 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/44 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/45 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/45 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/46 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/46 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/47 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/47 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/48 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/48 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/49 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/49 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/50 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/50 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/51 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/51 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/52 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/52 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/53 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/53 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/54 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/54 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/55 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/55 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/56 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/56 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/57 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/57 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/58 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/58 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/59 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/59 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/60 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/60 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/61 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/61 (36 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/62 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/62 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/63 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/63 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/64 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/64 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/65 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/65 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/66 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/66 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/67 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/67 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/68 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/68 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/69 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/69 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/70 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/70 (24 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/71 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/71 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/72 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/72 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/73 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/73 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/74 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/74 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/75 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/75 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/76 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/76 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/77 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/77 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/78 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/78 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/79 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/79 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/80 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/80 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/81 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/81 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/82 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/82 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/83 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/83 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/84 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/84 (22 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/85 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/85 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/86 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/86 (19 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/87 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/87 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/88 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/88 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/89 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/89 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/90 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/90 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/91 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/91 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/92 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/92 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/93 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/93 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/94 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/94 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/95 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/95 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/96 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/96 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/97 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/97 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/98 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/98 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/99 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/99 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/100 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/100 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/101 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/101 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/102 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/102 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/103 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/103 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/104 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/104 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/105 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/105 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/106 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/106 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/107 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/107 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/108 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/108 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/109 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/109 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/110 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/110 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/111 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/111 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/112 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/112 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/113 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/113 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/114 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/114 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/115 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/115 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/116 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/116 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/117 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/117 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/118 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/118 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/119 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/119 (9 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/120 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/120 (44 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/121 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/121 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/122 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/122 (42 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/123 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/123 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/124 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/124 (47 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/125 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/125 (66 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/126 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/126 (99 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/127 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/127 (84 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/128 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/128 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/129 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/129 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/130 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/130 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/131 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/131 (8 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/132 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/132 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/133 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/133 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/134 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/134 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/135 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/135 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/136 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/136 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/137 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/137 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/138 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/138 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/139 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/139 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/140 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/140 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/141 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/141 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/142 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/142 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/143 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/143 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/144 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/144 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/145 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/145 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/146 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/146 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/147 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/147 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/148 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/148 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/149 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/149 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/150 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/150 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/151 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/151 (14 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/152 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/152 (17 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/153 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/153 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/154 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/154 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/155 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/155 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/156 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/156 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/157 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/157 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/158 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/158 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/159 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/159 (19 ms) 56: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB (4644 ms total) 56: 56: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 (47 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 (12 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 (23 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 (15 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 (13 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 (10 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 (11 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 (16 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 (29 ms) 56: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB (566 ms total) 56: 56: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 (26 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 (5 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 (33 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 708 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 (21 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 (53 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 (49 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 (41 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2066 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 (45 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 (61 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 (60 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 (76 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2564 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 (75 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 (74 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 (87 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 (89 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 (93 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 (18 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 798 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 (20 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 (31 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 (83 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 (79 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 (75 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 3419 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 (59 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 (63 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 (63 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 (46 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2923 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 (48 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 (102 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 (71 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 (134 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 (103 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 (97 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2745 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 (93 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 (71 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 (79 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1742 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1643 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 (38 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1380 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 (34 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1060 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 (27 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 (150 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 (201 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 (184 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 5347 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 (180 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 (44 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1264 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 (28 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 (30 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 (43 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 (46 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1429 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 (35 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 (25 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 (29 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 1285 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 (37 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 (56 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 (68 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 (72 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 56: WARNING: all CONECT records are ignored 56: Reading frames from pdb fileWARNING: all CONECT records are ignored 56: Reading frame 0 time 0.000 '', 2595 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 (67 ms) 56: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB (4538 ms total) 56: 56: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 (141 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 (149 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 (140 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 (146 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 (39 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 (55 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 (51 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 (32 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 (40 ms) 56: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 56: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 56: Last frame 0 time 500.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: W. Kabsch, C. Sander 56: Dictionary of protein secondary structure: pattern recognition of 56: hydrogen-bonded and geometrical features. 56: Biopolymers 22 (1983) pp. 2577-2637 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 56: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 56: Trajectories 56: Journal of Chemical Information and Modeling 0 (2024) pp. 0 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 (32 ms) 56: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB (913 ms total) 56: 56: [----------] 3 tests from GyrateTests/GyrateModuleTest 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (16 ms) 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (20 ms) 56: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (28 ms) 56: [----------] 3 tests from GyrateTests/GyrateModuleTest (64 ms total) 56: 56: [----------] 6 tests from HBondTests/HbondModuleTest 56: [ RUN ] HBondTests/HbondModuleTest.Works/0 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/0 (23 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/1 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/1 (19 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/2 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/2 (155 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/3 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 56: Merging hbonds with Acceptor and Donor swapped 56: [ OK ] HBondTests/HbondModuleTest.Works/3 (171 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/4 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/4 (154 ms) 56: [ RUN ] HBondTests/HbondModuleTest.Works/5 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 56: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 56: Analyzed 2 frames, last time 10.000 56: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 56: [ OK ] HBondTests/HbondModuleTest.Works/5 (165 ms) 56: [----------] 6 tests from HBondTests/HbondModuleTest (808 ms total) 56: 56: [----------] 4 tests from MoleculeTests/ScatteringModule 56: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (17 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: D. T. Cromer & J. B. Mann 56: X-ray scattering factors computed from numerical Hartree-Fock wave functions 56: Acta Cryst. A 24 (1968) pp. 321 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (714 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (21 ms) 56: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 56: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 56: Last frame 0 time 0.000 56: Analyzed 1 frames, last time 0.000 56: 56: WARNING: Masses and atomic (Van der Waals) radii will be guessed 56: based on residue and atom names, since they could not be 56: definitively assigned from the information in your input 56: files. These guessed numbers might deviate from the mass 56: and radius of the atom type. Please check the output 56: files if necessary. Note, that this functionality may 56: be removed in a future GROMACS version. Please, consider 56: using another file format for your input. 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 56: Method for calculating small-angle neutron scattering spectra using all-atom 56: molecular dynamics trajectories 56: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 56: -------- -------- --- Thank You --- -------- -------- 56: 56: 56: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 56: D. T. Cromer & J. B. Mann 56: X-ray scattering factors computed from numerical Hartree-Fock wave functions 56: Acta Cryst. A 24 (1968) pp. 321 56: -------- -------- --- Thank You --- -------- -------- 56: 56: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (171 ms) 56: [----------] 4 tests from MoleculeTests/ScatteringModule (943 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 385 tests from 24 test suites ran. (15607 ms total) 56: [ PASSED ] 385 tests. 56: 56: YOU HAVE 1 DISABLED TEST 56: 56/87 Test #56: TrajectoryAnalysisUnitTests ............... Passed 15.70 sec test 57 Start 57: EnergyAnalysisUnitTests 57: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests 57: Test timeout computed to be: 30 57: [==========] Running 11 tests from 5 test suites. 57: [----------] Global test environment set-up. 57: [----------] 2 tests from EnergyTermTest 57: [ RUN ] EnergyTermTest.ConstructWorks 57: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 57: [ RUN ] EnergyTermTest.AddFrameWorks 57: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 57: [----------] 2 tests from EnergyTermTest (0 ms total) 57: 57: [----------] 1 test from DhdlTest 57: [ RUN ] DhdlTest.ExtractDhdl 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 57: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 57: Note: file tpx version 110, software tpx version 134 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 57: 57: 57: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 57: [ OK ] DhdlTest.ExtractDhdl (20 ms) 57: [----------] 1 test from DhdlTest (20 ms total) 57: 57: [----------] 1 test from OriresTest 57: [ RUN ] OriresTest.ExtractOrires 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 57: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 57: Note: file tpx version 111, software tpx version 134 57: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 57: End your selection with 0 57: Selecting all 7 orientation restraints 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 57: [ OK ] OriresTest.ExtractOrires (46 ms) 57: [----------] 1 test from OriresTest (46 ms total) 57: 57: [----------] 5 tests from EnergyTest 57: [ RUN ] EnergyTest.ExtractEnergy 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 57: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 57: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 57: [ OK ] EnergyTest.ExtractEnergy (1 ms) 57: [ RUN ] EnergyTest.ExtractEnergyByNumber 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 57: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 57: Pres. DC -268.49 3 8.52175 13.2804 (bar) 57: [ OK ] EnergyTest.ExtractEnergyByNumber (17 ms) 57: [ RUN ] EnergyTest.ExtractEnergyMixed 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 57: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 57: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 57: 13 Box-Z 14 Volume 15 Density 16 pV 57: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 57: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 57: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 57: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 57: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 57: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: [ OK ] EnergyTest.ExtractEnergyMixed (1 ms) 57: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 57: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 57: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 57: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 57: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 57: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 57: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 57: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 57: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 57: 37 1/Viscosity 38 T-System 39 Lamb-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 57: 57: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 57: All statistics are over 3 points (frames) 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 57: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 57: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 57: 57: Select the terms you want from the following list by 57: selecting either (part of) the name or the number or a combination. 57: End your selection with an empty line or a zero. 57: ------------------------------------------------------------------- 57: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 57: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 57: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 57: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 57: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 57: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 57: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 57: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 57: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 57: 37 1/Viscosity 38 T-System 39 Lamb-System 57: 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 57: 57: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 57: All statistics are over 3 points (frames) 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 57: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 57: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 57: [----------] 5 tests from EnergyTest (20 ms total) 57: 57: [----------] 2 tests from ViscosityTest 57: [ RUN ] ViscosityTest.EinsteinViscosity 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Pres-XX 20.2092 65 717.193 185.978 (bar) 57: Pres-XY -47.7351 39 372.522 207.456 (bar) 57: Pres-XZ 11.477 31 379.79 6.80818 (bar) 57: Pres-YX -47.7106 39 372.525 207.5 (bar) 57: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 57: Pres-YZ -41.3534 45 401.216 114.663 (bar) 57: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 57: Pres-ZY -41.3119 45 401.196 114.743 (bar) 57: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 57: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: 57: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 57: [ OK ] ViscosityTest.EinsteinViscosity (157 ms) 57: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 57: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 57: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 57: 57: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 57: All statistics are over 5001 points 57: 57: Energy Average Err.Est. RMSD Tot-Drift 57: ------------------------------------------------------------------------------- 57: Pres-XX 20.2092 65 717.193 185.978 (bar) 57: Pres-XY -47.7351 39 372.522 207.456 (bar) 57: Pres-XZ 11.477 31 379.79 6.80818 (bar) 57: Pres-YX -47.7106 39 372.525 207.5 (bar) 57: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 57: Pres-YZ -41.3534 45 401.216 114.663 (bar) 57: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 57: Pres-ZY -41.3119 45 401.196 114.743 (bar) 57: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 57: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 57: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 57: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 57: 57: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 57: [ OK ] ViscosityTest.EinsteinViscosityIntegral (101 ms) 57: [----------] 2 tests from ViscosityTest (259 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 11 tests from 5 test suites ran. (347 ms total) 57: [ PASSED ] 11 tests. 57/87 Test #57: EnergyAnalysisUnitTests ................... Passed 0.42 sec test 58 Start 58: ToolUnitTests 58: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests 58: Test timeout computed to be: 1920 58: [==========] Running 62 tests from 7 test suites. 58: [----------] Global test environment set-up. 58: [----------] 2 tests from DumpTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Setting the LD random seed to -2359427 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ RUN ] DumpTest.WorksWithTpr 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 58: inputrec: 58: integrator = md 58: tinit = 0 58: dt = 0.001 58: nsteps = 0 58: init-step = 0 58: simulation-part = 1 58: mts = false 58: mass-repartition-factor = 1 58: comm-mode = Linear 58: nstcomm = 100 58: bd-fric = 0 58: ld-seed = -2359427 58: emtol = 10 58: emstep = 0.01 58: niter = 20 58: fcstep = 0 58: nstcgsteep = 1000 58: nbfgscorr = 10 58: rtpi = 0.05 58: nstxout = 0 58: nstvout = 0 58: nstfout = 0 58: nstlog = 1000 58: nstcalcenergy = 100 58: nstenergy = 1000 58: nstxout-compressed = 0 58: compressed-x-precision = 1000 58: cutoff-scheme = Verlet 58: nstlist = 10 58: pbc = xyz 58: periodic-molecules = false 58: verlet-buffer-tolerance = -1 58: verlet-buffer-pressure-tolerance = 0.5 58: rlist = 1.1 58: coulombtype = Cut-off 58: coulomb-modifier = Potential-shift 58: rcoulomb-switch = 0 58: rcoulomb = 1 58: epsilon-r = 1 58: epsilon-rf = inf 58: vdw-type = Cut-off 58: vdw-modifier = Potential-shift 58: rvdw-switch = 0 58: rvdw = 1 58: DispCorr = No 58: table-extension = 1 58: fourierspacing = 0.12 58: fourier-nx = 0 58: fourier-ny = 0 58: fourier-nz = 0 58: pme-order = 4 58: ewald-rtol = 1e-05 58: ewald-rtol-lj = 0.001 58: lj-pme-comb-rule = Geometric 58: ewald-geometry = 3d 58: epsilon-surface = 0 58: ensemble-temperature-setting = not available 58: tcoupl = No 58: nsttcouple = -1 58: nh-chain-length = 0 58: print-nose-hoover-chain-variables = false 58: pcoupl = No 58: refcoord-scaling = No 58: posres-com (3): 58: posres-com[0]= 0.00000e+00 58: posres-com[1]= 0.00000e+00 58: posres-com[2]= 0.00000e+00 58: posres-comB (3): 58: posres-comB[0]= 0.00000e+00 58: posres-comB[1]= 0.00000e+00 58: posres-comB[2]= 0.00000e+00 58: QMMM = false 58: qm-opts: 58: ngQM = 0 58: constraint-algorithm = Lincs 58: continuation = false 58: Shake-SOR = false 58: shake-tol = 0.0001 58: lincs-order = 4 58: lincs-iter = 1 58: lincs-warnangle = 30 58: nwall = 0 58: wall-type = 9-3 58: wall-r-linpot = -1 58: wall-atomtype[0] = -1 58: wall-atomtype[1] = -1 58: wall-density[0] = 0 58: wall-density[1] = 0 58: wall-ewald-zfac = 3 58: pull = false 58: awh = false 58: rotation = false 58: interactiveMD = false 58: disre = No 58: disre-weighting = Conservative 58: disre-mixed = false 58: dr-fc = 1000 58: dr-tau = 0 58: nstdisreout = 100 58: orire-fc = 0 58: orire-tau = 0 58: nstorireout = 100 58: free-energy = no 58: cos-acceleration = 0 58: deform (3x3): 58: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: simulated-tempering = false 58: swapcoords = no 58: userint1 = 0 58: userint2 = 0 58: userint3 = 0 58: userint4 = 0 58: userreal1 = 0 58: userreal2 = 0 58: userreal3 = 0 58: userreal4 = 0 58: applied-forces: 58: electric-field: 58: x: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: y: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: z: 58: E0 = 0 58: omega = 0 58: t0 = 0 58: sigma = 0 58: density-guided-simulation: 58: active = false 58: group = protein 58: similarity-measure = inner-product 58: atom-spreading-weight = unity 58: force-constant = 1e+09 58: gaussian-transform-spreading-width = 0.2 58: gaussian-transform-spreading-range-in-multiples-of-width = 4 58: reference-density-filename = reference.mrc 58: nst = 1 58: normalize-densities = true 58: adaptive-force-scaling = false 58: adaptive-force-scaling-time-constant = 4 58: shift-vector = 58: transformation-matrix = 58: qmmm-cp2k: 58: active = false 58: qmgroup = System 58: qmmethod = PBE 58: qmfilenames = 58: qmcharge = 0 58: qmmultiplicity = 1 58: colvars: 58: active = false 58: configfile = 58: seed = -1 58: grpopts: 58: nrdf: 465 58: ref-t: 0 58: tau-t: 0 58: annealing: No 58: annealing-npoints: 0 58: acc: 0 0 0 58: nfreeze: N N N 58: energygrp-flags[ 0]: 0 58: header: 58: bIr = present 58: bBox = present 58: bTop = present 58: bX = present 58: bV = present 58: bF = not present 58: natoms = 156 58: lambda = 0.000000e+00 58: buffer size = 56904 58: topology: 58: name="First 10 residues from 1AKI" 58: #atoms = 156 58: #molblock = 1 58: molblock (0): 58: moltype = 0 "Protein_chain_B" 58: #molecules = 1 58: #posres_xA = 0 58: #posres_xB = 0 58: bIntermolecularInteractions = false 58: ffparams: 58: atnr=10 58: ntypes=212 58: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06 58: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 58: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06 58: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07 58: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06 58: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06 58: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 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functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 58: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 58: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 58: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 58: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 58: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 58: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 58: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 58: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 58: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2 58: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2 58: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2 58: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 58: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 58: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07 58: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06 58: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06 58: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06 58: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 58: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07 58: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06 58: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08 58: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07 58: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06 58: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07 58: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06 58: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06 58: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06 58: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06 58: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07 58: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07 58: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07 58: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06 58: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06 58: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08 58: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07 58: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08 58: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06 58: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07 58: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05 58: reppow = 12 58: fudgeQQ = 0.5 58: cmap 58: moltype (0): 58: name="Protein_chain_B" 58: atoms: 58: atom (156): 58: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 58: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 58: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 58: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 58: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 58: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 58: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 58: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 58: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 58: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 58: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 58: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 58: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 58: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 58: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 58: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 58: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 58: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 58: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 58: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 58: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 58: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 58: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 58: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 58: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 58: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 58: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 58: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 58: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 58: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 58: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 58: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 58: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 58: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 58: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 58: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 58: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 58: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 58: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 58: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 58: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 58: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 58: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 58: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 58: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 58: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 58: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 58: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 58: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 58: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 58: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 58: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 58: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 58: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 58: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 58: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 58: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 58: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 58: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 58: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 58: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 58: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 58: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 58: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 58: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 58: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 58: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 58: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 58: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 58: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 58: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 58: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 58: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 58: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 58: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 58: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 58: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 58: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 58: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 58: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 58: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 58: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 58: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 58: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 58: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 58: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 58: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 58: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 58: atom (156): 58: atom[0]={name="N"} 58: atom[1]={name="H1"} 58: atom[2]={name="H2"} 58: atom[3]={name="H3"} 58: atom[4]={name="CA"} 58: atom[5]={name="HA"} 58: atom[6]={name="CB"} 58: atom[7]={name="HB1"} 58: atom[8]={name="HB2"} 58: atom[9]={name="CG"} 58: atom[10]={name="HG1"} 58: atom[11]={name="HG2"} 58: atom[12]={name="CD"} 58: atom[13]={name="HD1"} 58: atom[14]={name="HD2"} 58: atom[15]={name="CE"} 58: atom[16]={name="HE1"} 58: atom[17]={name="HE2"} 58: atom[18]={name="NZ"} 58: atom[19]={name="HZ1"} 58: atom[20]={name="HZ2"} 58: atom[21]={name="HZ3"} 58: atom[22]={name="C"} 58: atom[23]={name="O"} 58: atom[24]={name="N"} 58: atom[25]={name="H"} 58: atom[26]={name="CA"} 58: atom[27]={name="HA"} 58: atom[28]={name="CB"} 58: atom[29]={name="HB"} 58: atom[30]={name="CG1"} 58: atom[31]={name="HG11"} 58: atom[32]={name="HG12"} 58: atom[33]={name="HG13"} 58: atom[34]={name="CG2"} 58: atom[35]={name="HG21"} 58: atom[36]={name="HG22"} 58: atom[37]={name="HG23"} 58: atom[38]={name="C"} 58: atom[39]={name="O"} 58: atom[40]={name="N"} 58: atom[41]={name="H"} 58: atom[42]={name="CA"} 58: atom[43]={name="HA"} 58: atom[44]={name="CB"} 58: atom[45]={name="HB1"} 58: atom[46]={name="HB2"} 58: atom[47]={name="CG"} 58: atom[48]={name="CD1"} 58: atom[49]={name="HD1"} 58: atom[50]={name="CD2"} 58: atom[51]={name="HD2"} 58: atom[52]={name="CE1"} 58: atom[53]={name="HE1"} 58: atom[54]={name="CE2"} 58: atom[55]={name="HE2"} 58: atom[56]={name="CZ"} 58: atom[57]={name="HZ"} 58: atom[58]={name="C"} 58: atom[59]={name="O"} 58: atom[60]={name="N"} 58: atom[61]={name="H"} 58: atom[62]={name="CA"} 58: atom[63]={name="HA1"} 58: atom[64]={name="HA2"} 58: atom[65]={name="C"} 58: atom[66]={name="O"} 58: atom[67]={name="N"} 58: atom[68]={name="H"} 58: atom[69]={name="CA"} 58: atom[70]={name="HA"} 58: atom[71]={name="CB"} 58: atom[72]={name="HB1"} 58: atom[73]={name="HB2"} 58: atom[74]={name="CG"} 58: atom[75]={name="HG1"} 58: atom[76]={name="HG2"} 58: atom[77]={name="CD"} 58: atom[78]={name="HD1"} 58: atom[79]={name="HD2"} 58: atom[80]={name="NE"} 58: atom[81]={name="HE"} 58: atom[82]={name="CZ"} 58: atom[83]={name="NH1"} 58: atom[84]={name="HH11"} 58: atom[85]={name="HH12"} 58: atom[86]={name="NH2"} 58: atom[87]={name="HH21"} 58: atom[88]={name="HH22"} 58: atom[89]={name="C"} 58: atom[90]={name="O"} 58: atom[91]={name="N"} 58: atom[92]={name="H"} 58: atom[93]={name="CA"} 58: atom[94]={name="HA"} 58: atom[95]={name="CB"} 58: atom[96]={name="HB1"} 58: atom[97]={name="HB2"} 58: atom[98]={name="SG"} 58: atom[99]={name="HG"} 58: atom[100]={name="C"} 58: atom[101]={name="O"} 58: atom[102]={name="N"} 58: atom[103]={name="H"} 58: atom[104]={name="CA"} 58: atom[105]={name="HA"} 58: atom[106]={name="CB"} 58: atom[107]={name="HB1"} 58: atom[108]={name="HB2"} 58: atom[109]={name="CG"} 58: atom[110]={name="HG1"} 58: atom[111]={name="HG2"} 58: atom[112]={name="CD"} 58: atom[113]={name="OE1"} 58: atom[114]={name="OE2"} 58: atom[115]={name="C"} 58: atom[116]={name="O"} 58: atom[117]={name="N"} 58: atom[118]={name="H"} 58: atom[119]={name="CA"} 58: atom[120]={name="HA"} 58: atom[121]={name="CB"} 58: atom[122]={name="HB1"} 58: atom[123]={name="HB2"} 58: atom[124]={name="CG"} 58: atom[125]={name="HG"} 58: atom[126]={name="CD1"} 58: atom[127]={name="HD11"} 58: atom[128]={name="HD12"} 58: atom[129]={name="HD13"} 58: atom[130]={name="CD2"} 58: atom[131]={name="HD21"} 58: atom[132]={name="HD22"} 58: atom[133]={name="HD23"} 58: atom[134]={name="C"} 58: atom[135]={name="O"} 58: atom[136]={name="N"} 58: atom[137]={name="H"} 58: atom[138]={name="CA"} 58: atom[139]={name="HA"} 58: atom[140]={name="CB"} 58: atom[141]={name="HB1"} 58: atom[142]={name="HB2"} 58: atom[143]={name="HB3"} 58: atom[144]={name="C"} 58: atom[145]={name="O"} 58: atom[146]={name="N"} 58: atom[147]={name="H"} 58: atom[148]={name="CA"} 58: atom[149]={name="HA"} 58: atom[150]={name="CB"} 58: atom[151]={name="HB1"} 58: atom[152]={name="HB2"} 58: atom[153]={name="HB3"} 58: atom[154]={name="C"} 58: atom[155]={name="O"} 58: type (156): 58: type[0]={name="opls_287",nameB="opls_287"} 58: type[1]={name="opls_290",nameB="opls_290"} 58: type[2]={name="opls_290",nameB="opls_290"} 58: type[3]={name="opls_290",nameB="opls_290"} 58: type[4]={name="opls_293B",nameB="opls_293B"} 58: type[5]={name="opls_140",nameB="opls_140"} 58: type[6]={name="opls_136",nameB="opls_136"} 58: type[7]={name="opls_140",nameB="opls_140"} 58: type[8]={name="opls_140",nameB="opls_140"} 58: type[9]={name="opls_136",nameB="opls_136"} 58: type[10]={name="opls_140",nameB="opls_140"} 58: type[11]={name="opls_140",nameB="opls_140"} 58: type[12]={name="opls_136",nameB="opls_136"} 58: type[13]={name="opls_140",nameB="opls_140"} 58: type[14]={name="opls_140",nameB="opls_140"} 58: type[15]={name="opls_292",nameB="opls_292"} 58: type[16]={name="opls_140",nameB="opls_140"} 58: type[17]={name="opls_140",nameB="opls_140"} 58: type[18]={name="opls_287",nameB="opls_287"} 58: type[19]={name="opls_290",nameB="opls_290"} 58: type[20]={name="opls_290",nameB="opls_290"} 58: type[21]={name="opls_290",nameB="opls_290"} 58: type[22]={name="opls_235",nameB="opls_235"} 58: type[23]={name="opls_236",nameB="opls_236"} 58: type[24]={name="opls_238",nameB="opls_238"} 58: type[25]={name="opls_241",nameB="opls_241"} 58: type[26]={name="opls_224B",nameB="opls_224B"} 58: type[27]={name="opls_140",nameB="opls_140"} 58: type[28]={name="opls_137",nameB="opls_137"} 58: type[29]={name="opls_140",nameB="opls_140"} 58: type[30]={name="opls_135",nameB="opls_135"} 58: type[31]={name="opls_140",nameB="opls_140"} 58: type[32]={name="opls_140",nameB="opls_140"} 58: type[33]={name="opls_140",nameB="opls_140"} 58: type[34]={name="opls_135",nameB="opls_135"} 58: type[35]={name="opls_140",nameB="opls_140"} 58: type[36]={name="opls_140",nameB="opls_140"} 58: type[37]={name="opls_140",nameB="opls_140"} 58: type[38]={name="opls_235",nameB="opls_235"} 58: type[39]={name="opls_236",nameB="opls_236"} 58: type[40]={name="opls_238",nameB="opls_238"} 58: type[41]={name="opls_241",nameB="opls_241"} 58: type[42]={name="opls_224B",nameB="opls_224B"} 58: type[43]={name="opls_140",nameB="opls_140"} 58: type[44]={name="opls_149",nameB="opls_149"} 58: type[45]={name="opls_140",nameB="opls_140"} 58: type[46]={name="opls_140",nameB="opls_140"} 58: type[47]={name="opls_145",nameB="opls_145"} 58: type[48]={name="opls_145",nameB="opls_145"} 58: type[49]={name="opls_146",nameB="opls_146"} 58: type[50]={name="opls_145",nameB="opls_145"} 58: type[51]={name="opls_146",nameB="opls_146"} 58: type[52]={name="opls_145",nameB="opls_145"} 58: type[53]={name="opls_146",nameB="opls_146"} 58: type[54]={name="opls_145",nameB="opls_145"} 58: type[55]={name="opls_146",nameB="opls_146"} 58: type[56]={name="opls_145",nameB="opls_145"} 58: type[57]={name="opls_146",nameB="opls_146"} 58: type[58]={name="opls_235",nameB="opls_235"} 58: type[59]={name="opls_236",nameB="opls_236"} 58: type[60]={name="opls_238",nameB="opls_238"} 58: type[61]={name="opls_241",nameB="opls_241"} 58: type[62]={name="opls_223B",nameB="opls_223B"} 58: type[63]={name="opls_140",nameB="opls_140"} 58: type[64]={name="opls_140",nameB="opls_140"} 58: type[65]={name="opls_235",nameB="opls_235"} 58: type[66]={name="opls_236",nameB="opls_236"} 58: type[67]={name="opls_238",nameB="opls_238"} 58: type[68]={name="opls_241",nameB="opls_241"} 58: type[69]={name="opls_224B",nameB="opls_224B"} 58: type[70]={name="opls_140",nameB="opls_140"} 58: type[71]={name="opls_136",nameB="opls_136"} 58: type[72]={name="opls_140",nameB="opls_140"} 58: type[73]={name="opls_140",nameB="opls_140"} 58: type[74]={name="opls_308",nameB="opls_308"} 58: type[75]={name="opls_140",nameB="opls_140"} 58: type[76]={name="opls_140",nameB="opls_140"} 58: type[77]={name="opls_307",nameB="opls_307"} 58: type[78]={name="opls_140",nameB="opls_140"} 58: type[79]={name="opls_140",nameB="opls_140"} 58: type[80]={name="opls_303",nameB="opls_303"} 58: type[81]={name="opls_304",nameB="opls_304"} 58: type[82]={name="opls_302",nameB="opls_302"} 58: type[83]={name="opls_300",nameB="opls_300"} 58: type[84]={name="opls_301",nameB="opls_301"} 58: type[85]={name="opls_301",nameB="opls_301"} 58: type[86]={name="opls_300",nameB="opls_300"} 58: type[87]={name="opls_301",nameB="opls_301"} 58: type[88]={name="opls_301",nameB="opls_301"} 58: type[89]={name="opls_235",nameB="opls_235"} 58: type[90]={name="opls_236",nameB="opls_236"} 58: type[91]={name="opls_238",nameB="opls_238"} 58: type[92]={name="opls_241",nameB="opls_241"} 58: type[93]={name="opls_224B",nameB="opls_224B"} 58: type[94]={name="opls_140",nameB="opls_140"} 58: type[95]={name="opls_206",nameB="opls_206"} 58: type[96]={name="opls_140",nameB="opls_140"} 58: type[97]={name="opls_140",nameB="opls_140"} 58: type[98]={name="opls_200",nameB="opls_200"} 58: type[99]={name="opls_204",nameB="opls_204"} 58: type[100]={name="opls_235",nameB="opls_235"} 58: type[101]={name="opls_236",nameB="opls_236"} 58: type[102]={name="opls_238",nameB="opls_238"} 58: type[103]={name="opls_241",nameB="opls_241"} 58: type[104]={name="opls_224B",nameB="opls_224B"} 58: type[105]={name="opls_140",nameB="opls_140"} 58: type[106]={name="opls_136",nameB="opls_136"} 58: type[107]={name="opls_140",nameB="opls_140"} 58: type[108]={name="opls_140",nameB="opls_140"} 58: type[109]={name="opls_274",nameB="opls_274"} 58: type[110]={name="opls_140",nameB="opls_140"} 58: type[111]={name="opls_140",nameB="opls_140"} 58: type[112]={name="opls_271",nameB="opls_271"} 58: type[113]={name="opls_272",nameB="opls_272"} 58: type[114]={name="opls_272",nameB="opls_272"} 58: type[115]={name="opls_235",nameB="opls_235"} 58: type[116]={name="opls_236",nameB="opls_236"} 58: type[117]={name="opls_238",nameB="opls_238"} 58: type[118]={name="opls_241",nameB="opls_241"} 58: type[119]={name="opls_224B",nameB="opls_224B"} 58: type[120]={name="opls_140",nameB="opls_140"} 58: type[121]={name="opls_136",nameB="opls_136"} 58: type[122]={name="opls_140",nameB="opls_140"} 58: type[123]={name="opls_140",nameB="opls_140"} 58: type[124]={name="opls_137",nameB="opls_137"} 58: type[125]={name="opls_140",nameB="opls_140"} 58: type[126]={name="opls_135",nameB="opls_135"} 58: type[127]={name="opls_140",nameB="opls_140"} 58: type[128]={name="opls_140",nameB="opls_140"} 58: type[129]={name="opls_140",nameB="opls_140"} 58: type[130]={name="opls_135",nameB="opls_135"} 58: type[131]={name="opls_140",nameB="opls_140"} 58: type[132]={name="opls_140",nameB="opls_140"} 58: type[133]={name="opls_140",nameB="opls_140"} 58: type[134]={name="opls_235",nameB="opls_235"} 58: type[135]={name="opls_236",nameB="opls_236"} 58: type[136]={name="opls_238",nameB="opls_238"} 58: type[137]={name="opls_241",nameB="opls_241"} 58: type[138]={name="opls_224B",nameB="opls_224B"} 58: type[139]={name="opls_140",nameB="opls_140"} 58: type[140]={name="opls_135",nameB="opls_135"} 58: type[141]={name="opls_140",nameB="opls_140"} 58: type[142]={name="opls_140",nameB="opls_140"} 58: type[143]={name="opls_140",nameB="opls_140"} 58: type[144]={name="opls_235",nameB="opls_235"} 58: type[145]={name="opls_236",nameB="opls_236"} 58: type[146]={name="opls_238",nameB="opls_238"} 58: type[147]={name="opls_241",nameB="opls_241"} 58: type[148]={name="opls_224B",nameB="opls_224B"} 58: type[149]={name="opls_140",nameB="opls_140"} 58: type[150]={name="opls_135",nameB="opls_135"} 58: type[151]={name="opls_140",nameB="opls_140"} 58: type[152]={name="opls_140",nameB="opls_140"} 58: type[153]={name="opls_140",nameB="opls_140"} 58: type[154]={name="opls_235",nameB="opls_235"} 58: type[155]={name="opls_236",nameB="opls_236"} 58: residue (10): 58: residue[0]={name="LYS", nr=1, ic=' '} 58: residue[1]={name="VAL", nr=2, ic=' '} 58: residue[2]={name="PHE", nr=3, ic=' '} 58: residue[3]={name="GLY", nr=4, ic=' '} 58: residue[4]={name="ARG", nr=5, ic=' '} 58: residue[5]={name="CYS", nr=6, ic=' '} 58: residue[6]={name="GLU", nr=7, ic=' '} 58: residue[7]={name="LEU", nr=8, ic=' '} 58: residue[8]={name="ALA", nr=9, ic=' '} 58: residue[9]={name="ALA", nr=10, ic=' '} 58: excls: 58: numLists=156 58: numElements=1828 58: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 58: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 58: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 58: 23, 24, 25, 26} 58: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 58: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 58: 14, 15, 22, 23, 24} 58: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 58: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 58: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 58: 16, 17, 18, 22} 58: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 58: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 58: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 58: 17, 18, 19, 20, 21} 58: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 58: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 58: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 58: 20, 21} 58: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 58: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 58: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 58: 26, 27, 28, 38} 58: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 58: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 58: 30, 34, 38, 39, 40} 58: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 58: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 58: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 58: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 58: 40} 58: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 58: 34, 35, 36, 37, 38, 39, 40} 58: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 58: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 58: 36, 37, 38} 58: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 58: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 58: 40, 41, 42, 43, 44, 58} 58: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 58: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 58: 45, 46, 47, 58, 59, 60} 58: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 58: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58: 48, 50, 58, 59, 60, 61, 62} 58: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 58: 60} 58: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 58: 50, 51, 52, 54, 58, 59, 60} 58: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 58: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 58: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 58: 52, 53, 54, 55, 56, 58} 58: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58: 54, 56, 57} 58: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 58: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 58: 55, 56, 57} 58: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 58: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 58: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 58: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 58: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 58: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 58: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 58: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 58: 60, 61, 62, 63, 64, 65} 58: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 58: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 58: 65, 66, 67} 58: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 58: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 58: 68, 69} 58: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 58: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 58: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 58: 70, 71, 89} 58: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 58: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 58: 72, 73, 74, 89, 90, 91} 58: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 58: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 58: 75, 76, 77, 89, 90, 91, 92, 93} 58: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 58: 91} 58: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 58: 77, 78, 79, 80, 89, 90, 91} 58: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 58: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 58: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 58: 79, 80, 81, 82, 89} 58: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 58: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 58: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 58: 81, 82, 83, 86} 58: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 58: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 58: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 58: 84, 85, 86, 87, 88} 58: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 58: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 58: 87, 88} 58: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 58: excls[84][num=6]={80, 82, 83, 84, 85, 86} 58: excls[85][num=6]={80, 82, 83, 84, 85, 86} 58: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 58: excls[87][num=6]={80, 82, 83, 86, 87, 88} 58: excls[88][num=6]={80, 82, 83, 86, 87, 88} 58: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 58: 91, 92, 93, 94, 95, 100} 58: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 58: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 58: 96, 97, 98, 100, 101, 102} 58: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 58: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 58: 99, 100, 101, 102, 103, 104} 58: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 58: 102} 58: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 58: 101, 102} 58: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 58: excls[99][num=6]={93, 95, 96, 97, 98, 99} 58: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 58: 102, 103, 104, 105, 106, 115} 58: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 58: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 58: 106, 107, 108, 109, 115, 116, 117} 58: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 58: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 58: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 58: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 115, 116, 117} 58: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 110, 111, 112, 113, 114, 115, 116, 117} 58: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 115} 58: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 115} 58: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 58: 112, 113, 114, 115} 58: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 58: 114} 58: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 58: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 58: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 58: 115, 116, 117, 118, 119, 120, 121, 134} 58: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 58: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 58: 120, 121, 122, 123, 124, 134, 135, 136} 58: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 58: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 58: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 58: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 134, 135, 136} 58: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 58: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 130, 134} 58: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 130, 134} 58: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 58: 127, 128, 129, 130, 131, 132, 133, 134} 58: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 58: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 58: 129, 130, 131, 132, 133} 58: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 58: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 58: 134, 135, 136, 137, 138, 139, 140, 144} 58: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 58: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 58: 139, 140, 141, 142, 143, 144, 145, 146} 58: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 58: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 58: 142, 143, 144, 145, 146, 147, 148} 58: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146} 58: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146} 58: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 58: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 58: 144, 145, 146, 147, 148, 149, 150, 154} 58: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 58: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 58: 149, 150, 151, 152, 153, 154, 155} 58: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 58: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 58: 152, 153, 154, 155} 58: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 58: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 58: 154, 155} 58: excls[155][num=6]={146, 148, 149, 150, 154, 155} 58: Bond: 58: nr: 468 58: iatoms: 58: 0 type=100 (BONDS) 0 1 58: 1 type=100 (BONDS) 0 2 58: 2 type=100 (BONDS) 0 3 58: 3 type=101 (BONDS) 0 4 58: 4 type=102 (BONDS) 4 5 58: 5 type=103 (BONDS) 4 6 58: 6 type=104 (BONDS) 4 22 58: 7 type=102 (BONDS) 6 7 58: 8 type=102 (BONDS) 6 8 58: 9 type=103 (BONDS) 6 9 58: 10 type=102 (BONDS) 9 10 58: 11 type=102 (BONDS) 9 11 58: 12 type=103 (BONDS) 9 12 58: 13 type=102 (BONDS) 12 13 58: 14 type=102 (BONDS) 12 14 58: 15 type=103 (BONDS) 12 15 58: 16 type=102 (BONDS) 15 16 58: 17 type=102 (BONDS) 15 17 58: 18 type=101 (BONDS) 15 18 58: 19 type=100 (BONDS) 18 19 58: 20 type=100 (BONDS) 18 20 58: 21 type=100 (BONDS) 18 21 58: 22 type=105 (BONDS) 22 23 58: 23 type=106 (BONDS) 22 24 58: 24 type=100 (BONDS) 24 25 58: 25 type=107 (BONDS) 24 26 58: 26 type=102 (BONDS) 26 27 58: 27 type=103 (BONDS) 26 28 58: 28 type=104 (BONDS) 26 38 58: 29 type=102 (BONDS) 28 29 58: 30 type=103 (BONDS) 28 30 58: 31 type=103 (BONDS) 28 34 58: 32 type=102 (BONDS) 30 31 58: 33 type=102 (BONDS) 30 32 58: 34 type=102 (BONDS) 30 33 58: 35 type=102 (BONDS) 34 35 58: 36 type=102 (BONDS) 34 36 58: 37 type=102 (BONDS) 34 37 58: 38 type=105 (BONDS) 38 39 58: 39 type=106 (BONDS) 38 40 58: 40 type=100 (BONDS) 40 41 58: 41 type=107 (BONDS) 40 42 58: 42 type=102 (BONDS) 42 43 58: 43 type=103 (BONDS) 42 44 58: 44 type=104 (BONDS) 42 58 58: 45 type=102 (BONDS) 44 45 58: 46 type=102 (BONDS) 44 46 58: 47 type=108 (BONDS) 44 47 58: 48 type=109 (BONDS) 47 48 58: 49 type=109 (BONDS) 47 50 58: 50 type=110 (BONDS) 48 49 58: 51 type=109 (BONDS) 48 52 58: 52 type=110 (BONDS) 50 51 58: 53 type=109 (BONDS) 50 54 58: 54 type=110 (BONDS) 52 53 58: 55 type=109 (BONDS) 52 56 58: 56 type=110 (BONDS) 54 55 58: 57 type=109 (BONDS) 54 56 58: 58 type=110 (BONDS) 56 57 58: 59 type=105 (BONDS) 58 59 58: 60 type=106 (BONDS) 58 60 58: 61 type=100 (BONDS) 60 61 58: 62 type=107 (BONDS) 60 62 58: 63 type=102 (BONDS) 62 63 58: 64 type=102 (BONDS) 62 64 58: 65 type=104 (BONDS) 62 65 58: 66 type=105 (BONDS) 65 66 58: 67 type=106 (BONDS) 65 67 58: 68 type=100 (BONDS) 67 68 58: 69 type=107 (BONDS) 67 69 58: 70 type=102 (BONDS) 69 70 58: 71 type=103 (BONDS) 69 71 58: 72 type=104 (BONDS) 69 89 58: 73 type=102 (BONDS) 71 72 58: 74 type=102 (BONDS) 71 73 58: 75 type=103 (BONDS) 71 74 58: 76 type=102 (BONDS) 74 75 58: 77 type=102 (BONDS) 74 76 58: 78 type=103 (BONDS) 74 77 58: 79 type=102 (BONDS) 77 78 58: 80 type=102 (BONDS) 77 79 58: 81 type=111 (BONDS) 77 80 58: 82 type=100 (BONDS) 80 81 58: 83 type=112 (BONDS) 80 82 58: 84 type=112 (BONDS) 82 83 58: 85 type=112 (BONDS) 82 86 58: 86 type=100 (BONDS) 83 84 58: 87 type=100 (BONDS) 83 85 58: 88 type=100 (BONDS) 86 87 58: 89 type=100 (BONDS) 86 88 58: 90 type=105 (BONDS) 89 90 58: 91 type=106 (BONDS) 89 91 58: 92 type=100 (BONDS) 91 92 58: 93 type=107 (BONDS) 91 93 58: 94 type=102 (BONDS) 93 94 58: 95 type=103 (BONDS) 93 95 58: 96 type=104 (BONDS) 93 100 58: 97 type=102 (BONDS) 95 96 58: 98 type=102 (BONDS) 95 97 58: 99 type=113 (BONDS) 95 98 58: 100 type=114 (BONDS) 98 99 58: 101 type=105 (BONDS) 100 101 58: 102 type=106 (BONDS) 100 102 58: 103 type=100 (BONDS) 102 103 58: 104 type=107 (BONDS) 102 104 58: 105 type=102 (BONDS) 104 105 58: 106 type=103 (BONDS) 104 106 58: 107 type=104 (BONDS) 104 115 58: 108 type=102 (BONDS) 106 107 58: 109 type=102 (BONDS) 106 108 58: 110 type=103 (BONDS) 106 109 58: 111 type=102 (BONDS) 109 110 58: 112 type=102 (BONDS) 109 111 58: 113 type=104 (BONDS) 109 112 58: 114 type=115 (BONDS) 112 113 58: 115 type=115 (BONDS) 112 114 58: 116 type=105 (BONDS) 115 116 58: 117 type=106 (BONDS) 115 117 58: 118 type=100 (BONDS) 117 118 58: 119 type=107 (BONDS) 117 119 58: 120 type=102 (BONDS) 119 120 58: 121 type=103 (BONDS) 119 121 58: 122 type=104 (BONDS) 119 134 58: 123 type=102 (BONDS) 121 122 58: 124 type=102 (BONDS) 121 123 58: 125 type=103 (BONDS) 121 124 58: 126 type=102 (BONDS) 124 125 58: 127 type=103 (BONDS) 124 126 58: 128 type=103 (BONDS) 124 130 58: 129 type=102 (BONDS) 126 127 58: 130 type=102 (BONDS) 126 128 58: 131 type=102 (BONDS) 126 129 58: 132 type=102 (BONDS) 130 131 58: 133 type=102 (BONDS) 130 132 58: 134 type=102 (BONDS) 130 133 58: 135 type=105 (BONDS) 134 135 58: 136 type=106 (BONDS) 134 136 58: 137 type=100 (BONDS) 136 137 58: 138 type=107 (BONDS) 136 138 58: 139 type=102 (BONDS) 138 139 58: 140 type=103 (BONDS) 138 140 58: 141 type=104 (BONDS) 138 144 58: 142 type=102 (BONDS) 140 141 58: 143 type=102 (BONDS) 140 142 58: 144 type=102 (BONDS) 140 143 58: 145 type=105 (BONDS) 144 145 58: 146 type=106 (BONDS) 144 146 58: 147 type=100 (BONDS) 146 147 58: 148 type=107 (BONDS) 146 148 58: 149 type=102 (BONDS) 148 149 58: 150 type=103 (BONDS) 148 150 58: 151 type=104 (BONDS) 148 154 58: 152 type=102 (BONDS) 150 151 58: 153 type=102 (BONDS) 150 152 58: 154 type=102 (BONDS) 150 153 58: 155 type=105 (BONDS) 154 155 58: G96Bond: 58: nr: 0 58: Morse: 58: nr: 0 58: Cubic Bonds: 58: nr: 0 58: Connect Bonds: 58: nr: 0 58: Harmonic Pot.: 58: nr: 0 58: FENE Bonds: 58: nr: 0 58: Tab. Bonds: 58: nr: 0 58: Tab. Bonds NC: 58: nr: 0 58: Restraint Pot.: 58: nr: 0 58: Angle: 58: nr: 1124 58: iatoms: 58: 0 type=116 (ANGLES) 1 0 2 58: 1 type=116 (ANGLES) 1 0 3 58: 2 type=116 (ANGLES) 1 0 4 58: 3 type=116 (ANGLES) 2 0 3 58: 4 type=116 (ANGLES) 2 0 4 58: 5 type=116 (ANGLES) 3 0 4 58: 6 type=116 (ANGLES) 0 4 5 58: 7 type=117 (ANGLES) 0 4 6 58: 8 type=117 (ANGLES) 0 4 22 58: 9 type=118 (ANGLES) 5 4 6 58: 10 type=116 (ANGLES) 5 4 22 58: 11 type=119 (ANGLES) 6 4 22 58: 12 type=118 (ANGLES) 4 6 7 58: 13 type=118 (ANGLES) 4 6 8 58: 14 type=120 (ANGLES) 4 6 9 58: 15 type=121 (ANGLES) 7 6 8 58: 16 type=118 (ANGLES) 7 6 9 58: 17 type=118 (ANGLES) 8 6 9 58: 18 type=118 (ANGLES) 6 9 10 58: 19 type=118 (ANGLES) 6 9 11 58: 20 type=120 (ANGLES) 6 9 12 58: 21 type=121 (ANGLES) 10 9 11 58: 22 type=118 (ANGLES) 10 9 12 58: 23 type=118 (ANGLES) 11 9 12 58: 24 type=118 (ANGLES) 9 12 13 58: 25 type=118 (ANGLES) 9 12 14 58: 26 type=120 (ANGLES) 9 12 15 58: 27 type=121 (ANGLES) 13 12 14 58: 28 type=118 (ANGLES) 13 12 15 58: 29 type=118 (ANGLES) 14 12 15 58: 30 type=118 (ANGLES) 12 15 16 58: 31 type=118 (ANGLES) 12 15 17 58: 32 type=117 (ANGLES) 12 15 18 58: 33 type=121 (ANGLES) 16 15 17 58: 34 type=116 (ANGLES) 16 15 18 58: 35 type=116 (ANGLES) 17 15 18 58: 36 type=116 (ANGLES) 15 18 19 58: 37 type=116 (ANGLES) 15 18 20 58: 38 type=116 (ANGLES) 15 18 21 58: 39 type=116 (ANGLES) 19 18 20 58: 40 type=116 (ANGLES) 19 18 21 58: 41 type=116 (ANGLES) 20 18 21 58: 42 type=122 (ANGLES) 4 22 23 58: 43 type=123 (ANGLES) 4 22 24 58: 44 type=124 (ANGLES) 23 22 24 58: 45 type=125 (ANGLES) 22 24 25 58: 46 type=126 (ANGLES) 22 24 26 58: 47 type=127 (ANGLES) 25 24 26 58: 48 type=116 (ANGLES) 24 26 27 58: 49 type=128 (ANGLES) 24 26 28 58: 50 type=129 (ANGLES) 24 26 38 58: 51 type=118 (ANGLES) 27 26 28 58: 52 type=116 (ANGLES) 27 26 38 58: 53 type=119 (ANGLES) 28 26 38 58: 54 type=118 (ANGLES) 26 28 29 58: 55 type=120 (ANGLES) 26 28 30 58: 56 type=120 (ANGLES) 26 28 34 58: 57 type=118 (ANGLES) 29 28 30 58: 58 type=118 (ANGLES) 29 28 34 58: 59 type=120 (ANGLES) 30 28 34 58: 60 type=118 (ANGLES) 28 30 31 58: 61 type=118 (ANGLES) 28 30 32 58: 62 type=118 (ANGLES) 28 30 33 58: 63 type=121 (ANGLES) 31 30 32 58: 64 type=121 (ANGLES) 31 30 33 58: 65 type=121 (ANGLES) 32 30 33 58: 66 type=118 (ANGLES) 28 34 35 58: 67 type=118 (ANGLES) 28 34 36 58: 68 type=118 (ANGLES) 28 34 37 58: 69 type=121 (ANGLES) 35 34 36 58: 70 type=121 (ANGLES) 35 34 37 58: 71 type=121 (ANGLES) 36 34 37 58: 72 type=122 (ANGLES) 26 38 39 58: 73 type=123 (ANGLES) 26 38 40 58: 74 type=124 (ANGLES) 39 38 40 58: 75 type=125 (ANGLES) 38 40 41 58: 76 type=126 (ANGLES) 38 40 42 58: 77 type=127 (ANGLES) 41 40 42 58: 78 type=116 (ANGLES) 40 42 43 58: 79 type=128 (ANGLES) 40 42 44 58: 80 type=129 (ANGLES) 40 42 58 58: 81 type=118 (ANGLES) 43 42 44 58: 82 type=116 (ANGLES) 43 42 58 58: 83 type=119 (ANGLES) 44 42 58 58: 84 type=118 (ANGLES) 42 44 45 58: 85 type=118 (ANGLES) 42 44 46 58: 86 type=130 (ANGLES) 42 44 47 58: 87 type=121 (ANGLES) 45 44 46 58: 88 type=116 (ANGLES) 45 44 47 58: 89 type=116 (ANGLES) 46 44 47 58: 90 type=131 (ANGLES) 44 47 48 58: 91 type=131 (ANGLES) 44 47 50 58: 92 type=132 (ANGLES) 48 47 50 58: 93 type=133 (ANGLES) 47 48 49 58: 94 type=132 (ANGLES) 47 48 52 58: 95 type=133 (ANGLES) 49 48 52 58: 96 type=133 (ANGLES) 47 50 51 58: 97 type=132 (ANGLES) 47 50 54 58: 98 type=133 (ANGLES) 51 50 54 58: 99 type=133 (ANGLES) 48 52 53 58: 100 type=132 (ANGLES) 48 52 56 58: 101 type=133 (ANGLES) 53 52 56 58: 102 type=133 (ANGLES) 50 54 55 58: 103 type=132 (ANGLES) 50 54 56 58: 104 type=133 (ANGLES) 55 54 56 58: 105 type=132 (ANGLES) 52 56 54 58: 106 type=133 (ANGLES) 52 56 57 58: 107 type=133 (ANGLES) 54 56 57 58: 108 type=122 (ANGLES) 42 58 59 58: 109 type=123 (ANGLES) 42 58 60 58: 110 type=124 (ANGLES) 59 58 60 58: 111 type=125 (ANGLES) 58 60 61 58: 112 type=126 (ANGLES) 58 60 62 58: 113 type=127 (ANGLES) 61 60 62 58: 114 type=116 (ANGLES) 60 62 63 58: 115 type=116 (ANGLES) 60 62 64 58: 116 type=129 (ANGLES) 60 62 65 58: 117 type=121 (ANGLES) 63 62 64 58: 118 type=116 (ANGLES) 63 62 65 58: 119 type=116 (ANGLES) 64 62 65 58: 120 type=122 (ANGLES) 62 65 66 58: 121 type=123 (ANGLES) 62 65 67 58: 122 type=124 (ANGLES) 66 65 67 58: 123 type=125 (ANGLES) 65 67 68 58: 124 type=126 (ANGLES) 65 67 69 58: 125 type=127 (ANGLES) 68 67 69 58: 126 type=116 (ANGLES) 67 69 70 58: 127 type=128 (ANGLES) 67 69 71 58: 128 type=129 (ANGLES) 67 69 89 58: 129 type=118 (ANGLES) 70 69 71 58: 130 type=116 (ANGLES) 70 69 89 58: 131 type=119 (ANGLES) 71 69 89 58: 132 type=118 (ANGLES) 69 71 72 58: 133 type=118 (ANGLES) 69 71 73 58: 134 type=120 (ANGLES) 69 71 74 58: 135 type=121 (ANGLES) 72 71 73 58: 136 type=118 (ANGLES) 72 71 74 58: 137 type=118 (ANGLES) 73 71 74 58: 138 type=118 (ANGLES) 71 74 75 58: 139 type=118 (ANGLES) 71 74 76 58: 140 type=120 (ANGLES) 71 74 77 58: 141 type=121 (ANGLES) 75 74 76 58: 142 type=118 (ANGLES) 75 74 77 58: 143 type=118 (ANGLES) 76 74 77 58: 144 type=118 (ANGLES) 74 77 78 58: 145 type=118 (ANGLES) 74 77 79 58: 146 type=117 (ANGLES) 74 77 80 58: 147 type=121 (ANGLES) 78 77 79 58: 148 type=116 (ANGLES) 78 77 80 58: 149 type=116 (ANGLES) 79 77 80 58: 150 type=134 (ANGLES) 77 80 81 58: 151 type=135 (ANGLES) 77 80 82 58: 152 type=133 (ANGLES) 81 80 82 58: 153 type=131 (ANGLES) 80 82 83 58: 154 type=131 (ANGLES) 80 82 86 58: 155 type=131 (ANGLES) 83 82 86 58: 156 type=133 (ANGLES) 82 83 84 58: 157 type=133 (ANGLES) 82 83 85 58: 158 type=133 (ANGLES) 84 83 85 58: 159 type=133 (ANGLES) 82 86 87 58: 160 type=133 (ANGLES) 82 86 88 58: 161 type=133 (ANGLES) 87 86 88 58: 162 type=122 (ANGLES) 69 89 90 58: 163 type=123 (ANGLES) 69 89 91 58: 164 type=124 (ANGLES) 90 89 91 58: 165 type=125 (ANGLES) 89 91 92 58: 166 type=126 (ANGLES) 89 91 93 58: 167 type=127 (ANGLES) 92 91 93 58: 168 type=116 (ANGLES) 91 93 94 58: 169 type=128 (ANGLES) 91 93 95 58: 170 type=129 (ANGLES) 91 93 100 58: 171 type=118 (ANGLES) 94 93 95 58: 172 type=116 (ANGLES) 94 93 100 58: 173 type=119 (ANGLES) 95 93 100 58: 174 type=118 (ANGLES) 93 95 96 58: 175 type=118 (ANGLES) 93 95 97 58: 176 type=136 (ANGLES) 93 95 98 58: 177 type=121 (ANGLES) 96 95 97 58: 178 type=116 (ANGLES) 96 95 98 58: 179 type=116 (ANGLES) 97 95 98 58: 180 type=137 (ANGLES) 95 98 99 58: 181 type=122 (ANGLES) 93 100 101 58: 182 type=123 (ANGLES) 93 100 102 58: 183 type=124 (ANGLES) 101 100 102 58: 184 type=125 (ANGLES) 100 102 103 58: 185 type=126 (ANGLES) 100 102 104 58: 186 type=127 (ANGLES) 103 102 104 58: 187 type=116 (ANGLES) 102 104 105 58: 188 type=128 (ANGLES) 102 104 106 58: 189 type=129 (ANGLES) 102 104 115 58: 190 type=118 (ANGLES) 105 104 106 58: 191 type=116 (ANGLES) 105 104 115 58: 192 type=119 (ANGLES) 106 104 115 58: 193 type=118 (ANGLES) 104 106 107 58: 194 type=118 (ANGLES) 104 106 108 58: 195 type=120 (ANGLES) 104 106 109 58: 196 type=121 (ANGLES) 107 106 108 58: 197 type=118 (ANGLES) 107 106 109 58: 198 type=118 (ANGLES) 108 106 109 58: 199 type=118 (ANGLES) 106 109 110 58: 200 type=118 (ANGLES) 106 109 111 58: 201 type=119 (ANGLES) 106 109 112 58: 202 type=121 (ANGLES) 110 109 111 58: 203 type=116 (ANGLES) 110 109 112 58: 204 type=116 (ANGLES) 111 109 112 58: 205 type=138 (ANGLES) 109 112 113 58: 206 type=138 (ANGLES) 109 112 114 58: 207 type=139 (ANGLES) 113 112 114 58: 208 type=122 (ANGLES) 104 115 116 58: 209 type=123 (ANGLES) 104 115 117 58: 210 type=124 (ANGLES) 116 115 117 58: 211 type=125 (ANGLES) 115 117 118 58: 212 type=126 (ANGLES) 115 117 119 58: 213 type=127 (ANGLES) 118 117 119 58: 214 type=116 (ANGLES) 117 119 120 58: 215 type=128 (ANGLES) 117 119 121 58: 216 type=129 (ANGLES) 117 119 134 58: 217 type=118 (ANGLES) 120 119 121 58: 218 type=116 (ANGLES) 120 119 134 58: 219 type=119 (ANGLES) 121 119 134 58: 220 type=118 (ANGLES) 119 121 122 58: 221 type=118 (ANGLES) 119 121 123 58: 222 type=120 (ANGLES) 119 121 124 58: 223 type=121 (ANGLES) 122 121 123 58: 224 type=118 (ANGLES) 122 121 124 58: 225 type=118 (ANGLES) 123 121 124 58: 226 type=118 (ANGLES) 121 124 125 58: 227 type=120 (ANGLES) 121 124 126 58: 228 type=120 (ANGLES) 121 124 130 58: 229 type=118 (ANGLES) 125 124 126 58: 230 type=118 (ANGLES) 125 124 130 58: 231 type=120 (ANGLES) 126 124 130 58: 232 type=118 (ANGLES) 124 126 127 58: 233 type=118 (ANGLES) 124 126 128 58: 234 type=118 (ANGLES) 124 126 129 58: 235 type=121 (ANGLES) 127 126 128 58: 236 type=121 (ANGLES) 127 126 129 58: 237 type=121 (ANGLES) 128 126 129 58: 238 type=118 (ANGLES) 124 130 131 58: 239 type=118 (ANGLES) 124 130 132 58: 240 type=118 (ANGLES) 124 130 133 58: 241 type=121 (ANGLES) 131 130 132 58: 242 type=121 (ANGLES) 131 130 133 58: 243 type=121 (ANGLES) 132 130 133 58: 244 type=122 (ANGLES) 119 134 135 58: 245 type=123 (ANGLES) 119 134 136 58: 246 type=124 (ANGLES) 135 134 136 58: 247 type=125 (ANGLES) 134 136 137 58: 248 type=126 (ANGLES) 134 136 138 58: 249 type=127 (ANGLES) 137 136 138 58: 250 type=116 (ANGLES) 136 138 139 58: 251 type=128 (ANGLES) 136 138 140 58: 252 type=129 (ANGLES) 136 138 144 58: 253 type=118 (ANGLES) 139 138 140 58: 254 type=116 (ANGLES) 139 138 144 58: 255 type=119 (ANGLES) 140 138 144 58: 256 type=118 (ANGLES) 138 140 141 58: 257 type=118 (ANGLES) 138 140 142 58: 258 type=118 (ANGLES) 138 140 143 58: 259 type=121 (ANGLES) 141 140 142 58: 260 type=121 (ANGLES) 141 140 143 58: 261 type=121 (ANGLES) 142 140 143 58: 262 type=122 (ANGLES) 138 144 145 58: 263 type=123 (ANGLES) 138 144 146 58: 264 type=124 (ANGLES) 145 144 146 58: 265 type=125 (ANGLES) 144 146 147 58: 266 type=126 (ANGLES) 144 146 148 58: 267 type=127 (ANGLES) 147 146 148 58: 268 type=116 (ANGLES) 146 148 149 58: 269 type=128 (ANGLES) 146 148 150 58: 270 type=129 (ANGLES) 146 148 154 58: 271 type=118 (ANGLES) 149 148 150 58: 272 type=116 (ANGLES) 149 148 154 58: 273 type=119 (ANGLES) 150 148 154 58: 274 type=118 (ANGLES) 148 150 151 58: 275 type=118 (ANGLES) 148 150 152 58: 276 type=118 (ANGLES) 148 150 153 58: 277 type=121 (ANGLES) 151 150 152 58: 278 type=121 (ANGLES) 151 150 153 58: 279 type=121 (ANGLES) 152 150 153 58: 280 type=122 (ANGLES) 148 154 155 58: G96Angle: 58: nr: 0 58: Restr. Angles: 58: nr: 0 58: Lin. Angle: 58: nr: 0 58: Bond-Cross: 58: nr: 0 58: BA-Cross: 58: nr: 0 58: U-B: 58: nr: 0 58: Quartic Angles: 58: nr: 0 58: Tab. Angles: 58: nr: 0 58: Proper Dih.: 58: nr: 145 58: iatoms: 58: 0 type=140 (PDIHS) 4 24 22 23 58: 1 type=141 (PDIHS) 22 26 24 25 58: 2 type=140 (PDIHS) 26 40 38 39 58: 3 type=141 (PDIHS) 38 42 40 41 58: 4 type=140 (PDIHS) 42 60 58 59 58: 5 type=142 (PDIHS) 44 47 50 48 58: 6 type=142 (PDIHS) 47 52 48 49 58: 7 type=142 (PDIHS) 47 54 50 51 58: 8 type=142 (PDIHS) 48 56 52 53 58: 9 type=142 (PDIHS) 50 56 54 55 58: 10 type=142 (PDIHS) 52 54 56 57 58: 11 type=141 (PDIHS) 58 62 60 61 58: 12 type=140 (PDIHS) 62 67 65 66 58: 13 type=141 (PDIHS) 65 69 67 68 58: 14 type=140 (PDIHS) 69 91 89 90 58: 15 type=141 (PDIHS) 77 82 80 81 58: 16 type=140 (PDIHS) 80 83 82 86 58: 17 type=141 (PDIHS) 82 84 83 85 58: 18 type=141 (PDIHS) 82 87 86 88 58: 19 type=141 (PDIHS) 89 93 91 92 58: 20 type=140 (PDIHS) 93 102 100 101 58: 21 type=141 (PDIHS) 100 104 102 103 58: 22 type=140 (PDIHS) 104 117 115 116 58: 23 type=140 (PDIHS) 109 113 112 114 58: 24 type=141 (PDIHS) 115 119 117 118 58: 25 type=140 (PDIHS) 119 136 134 135 58: 26 type=141 (PDIHS) 134 138 136 137 58: 27 type=140 (PDIHS) 138 146 144 145 58: 28 type=141 (PDIHS) 144 148 146 147 58: Ryckaert-Bell.: 58: nr: 1565 58: iatoms: 58: 0 type=143 (RBDIHS) 1 0 4 5 58: 1 type=144 (RBDIHS) 1 0 4 6 58: 2 type=144 (RBDIHS) 1 0 4 22 58: 3 type=143 (RBDIHS) 2 0 4 5 58: 4 type=144 (RBDIHS) 2 0 4 6 58: 5 type=144 (RBDIHS) 2 0 4 22 58: 6 type=143 (RBDIHS) 3 0 4 5 58: 7 type=144 (RBDIHS) 3 0 4 6 58: 8 type=144 (RBDIHS) 3 0 4 22 58: 9 type=145 (RBDIHS) 0 4 6 9 58: 10 type=146 (RBDIHS) 22 4 6 9 58: 11 type=147 (RBDIHS) 0 4 6 7 58: 12 type=147 (RBDIHS) 0 4 6 8 58: 13 type=148 (RBDIHS) 5 4 6 7 58: 14 type=148 (RBDIHS) 5 4 6 8 58: 15 type=148 (RBDIHS) 5 4 6 9 58: 16 type=149 (RBDIHS) 22 4 6 7 58: 17 type=149 (RBDIHS) 22 4 6 8 58: 18 type=150 (RBDIHS) 0 4 22 24 58: 19 type=151 (RBDIHS) 6 4 22 24 58: 20 type=148 (RBDIHS) 4 6 9 10 58: 21 type=148 (RBDIHS) 4 6 9 11 58: 22 type=152 (RBDIHS) 4 6 9 12 58: 23 type=148 (RBDIHS) 7 6 9 10 58: 24 type=148 (RBDIHS) 7 6 9 11 58: 25 type=148 (RBDIHS) 7 6 9 12 58: 26 type=148 (RBDIHS) 8 6 9 10 58: 27 type=148 (RBDIHS) 8 6 9 11 58: 28 type=148 (RBDIHS) 8 6 9 12 58: 29 type=148 (RBDIHS) 6 9 12 13 58: 30 type=148 (RBDIHS) 6 9 12 14 58: 31 type=152 (RBDIHS) 6 9 12 15 58: 32 type=148 (RBDIHS) 10 9 12 13 58: 33 type=148 (RBDIHS) 10 9 12 14 58: 34 type=148 (RBDIHS) 10 9 12 15 58: 35 type=148 (RBDIHS) 11 9 12 13 58: 36 type=148 (RBDIHS) 11 9 12 14 58: 37 type=148 (RBDIHS) 11 9 12 15 58: 38 type=148 (RBDIHS) 9 12 15 16 58: 39 type=148 (RBDIHS) 9 12 15 17 58: 40 type=153 (RBDIHS) 9 12 15 18 58: 41 type=148 (RBDIHS) 13 12 15 16 58: 42 type=148 (RBDIHS) 13 12 15 17 58: 43 type=154 (RBDIHS) 13 12 15 18 58: 44 type=148 (RBDIHS) 14 12 15 16 58: 45 type=148 (RBDIHS) 14 12 15 17 58: 46 type=154 (RBDIHS) 14 12 15 18 58: 47 type=144 (RBDIHS) 12 15 18 19 58: 48 type=144 (RBDIHS) 12 15 18 20 58: 49 type=144 (RBDIHS) 12 15 18 21 58: 50 type=143 (RBDIHS) 16 15 18 19 58: 51 type=143 (RBDIHS) 16 15 18 20 58: 52 type=143 (RBDIHS) 16 15 18 21 58: 53 type=143 (RBDIHS) 17 15 18 19 58: 54 type=143 (RBDIHS) 17 15 18 20 58: 55 type=143 (RBDIHS) 17 15 18 21 58: 56 type=155 (RBDIHS) 4 22 24 25 58: 57 type=156 (RBDIHS) 4 22 24 26 58: 58 type=155 (RBDIHS) 23 22 24 25 58: 59 type=157 (RBDIHS) 23 22 24 26 58: 60 type=158 (RBDIHS) 22 24 26 28 58: 61 type=159 (RBDIHS) 22 24 26 38 58: 62 type=160 (RBDIHS) 24 26 28 30 58: 63 type=160 (RBDIHS) 24 26 28 34 58: 64 type=161 (RBDIHS) 38 26 28 30 58: 65 type=161 (RBDIHS) 38 26 28 34 58: 66 type=147 (RBDIHS) 24 26 28 29 58: 67 type=148 (RBDIHS) 27 26 28 29 58: 68 type=148 (RBDIHS) 27 26 28 30 58: 69 type=148 (RBDIHS) 27 26 28 34 58: 70 type=149 (RBDIHS) 38 26 28 29 58: 71 type=150 (RBDIHS) 24 26 38 40 58: 72 type=151 (RBDIHS) 28 26 38 40 58: 73 type=148 (RBDIHS) 26 28 30 31 58: 74 type=148 (RBDIHS) 26 28 30 32 58: 75 type=148 (RBDIHS) 26 28 30 33 58: 76 type=148 (RBDIHS) 29 28 30 31 58: 77 type=148 (RBDIHS) 29 28 30 32 58: 78 type=148 (RBDIHS) 29 28 30 33 58: 79 type=148 (RBDIHS) 34 28 30 31 58: 80 type=148 (RBDIHS) 34 28 30 32 58: 81 type=148 (RBDIHS) 34 28 30 33 58: 82 type=148 (RBDIHS) 26 28 34 35 58: 83 type=148 (RBDIHS) 26 28 34 36 58: 84 type=148 (RBDIHS) 26 28 34 37 58: 85 type=148 (RBDIHS) 29 28 34 35 58: 86 type=148 (RBDIHS) 29 28 34 36 58: 87 type=148 (RBDIHS) 29 28 34 37 58: 88 type=148 (RBDIHS) 30 28 34 35 58: 89 type=148 (RBDIHS) 30 28 34 36 58: 90 type=148 (RBDIHS) 30 28 34 37 58: 91 type=155 (RBDIHS) 26 38 40 41 58: 92 type=156 (RBDIHS) 26 38 40 42 58: 93 type=155 (RBDIHS) 39 38 40 41 58: 94 type=157 (RBDIHS) 39 38 40 42 58: 95 type=158 (RBDIHS) 38 40 42 44 58: 96 type=159 (RBDIHS) 38 40 42 58 58: 97 type=147 (RBDIHS) 40 42 44 45 58: 98 type=147 (RBDIHS) 40 42 44 46 58: 99 type=162 (RBDIHS) 40 42 44 47 58: 100 type=148 (RBDIHS) 43 42 44 45 58: 101 type=148 (RBDIHS) 43 42 44 46 58: 102 type=163 (RBDIHS) 43 42 44 47 58: 103 type=149 (RBDIHS) 58 42 44 45 58: 104 type=149 (RBDIHS) 58 42 44 46 58: 105 type=164 (RBDIHS) 58 42 44 47 58: 106 type=150 (RBDIHS) 40 42 58 60 58: 107 type=151 (RBDIHS) 44 42 58 60 58: 108 type=165 (RBDIHS) 44 47 48 49 58: 109 type=165 (RBDIHS) 44 47 48 52 58: 110 type=165 (RBDIHS) 50 47 48 49 58: 111 type=165 (RBDIHS) 50 47 48 52 58: 112 type=165 (RBDIHS) 44 47 50 51 58: 113 type=165 (RBDIHS) 44 47 50 54 58: 114 type=165 (RBDIHS) 48 47 50 51 58: 115 type=165 (RBDIHS) 48 47 50 54 58: 116 type=165 (RBDIHS) 47 48 52 53 58: 117 type=165 (RBDIHS) 47 48 52 56 58: 118 type=165 (RBDIHS) 49 48 52 53 58: 119 type=165 (RBDIHS) 49 48 52 56 58: 120 type=165 (RBDIHS) 47 50 54 55 58: 121 type=165 (RBDIHS) 47 50 54 56 58: 122 type=165 (RBDIHS) 51 50 54 55 58: 123 type=165 (RBDIHS) 51 50 54 56 58: 124 type=165 (RBDIHS) 48 52 56 54 58: 125 type=165 (RBDIHS) 48 52 56 57 58: 126 type=165 (RBDIHS) 53 52 56 54 58: 127 type=165 (RBDIHS) 53 52 56 57 58: 128 type=165 (RBDIHS) 50 54 56 52 58: 129 type=165 (RBDIHS) 50 54 56 57 58: 130 type=165 (RBDIHS) 55 54 56 52 58: 131 type=165 (RBDIHS) 55 54 56 57 58: 132 type=155 (RBDIHS) 42 58 60 61 58: 133 type=156 (RBDIHS) 42 58 60 62 58: 134 type=155 (RBDIHS) 59 58 60 61 58: 135 type=157 (RBDIHS) 59 58 60 62 58: 136 type=159 (RBDIHS) 58 60 62 65 58: 137 type=150 (RBDIHS) 60 62 65 67 58: 138 type=155 (RBDIHS) 62 65 67 68 58: 139 type=156 (RBDIHS) 62 65 67 69 58: 140 type=155 (RBDIHS) 66 65 67 68 58: 141 type=157 (RBDIHS) 66 65 67 69 58: 142 type=158 (RBDIHS) 65 67 69 71 58: 143 type=159 (RBDIHS) 65 67 69 89 58: 144 type=166 (RBDIHS) 67 69 71 74 58: 145 type=167 (RBDIHS) 89 69 71 74 58: 146 type=147 (RBDIHS) 67 69 71 72 58: 147 type=147 (RBDIHS) 67 69 71 73 58: 148 type=148 (RBDIHS) 70 69 71 72 58: 149 type=148 (RBDIHS) 70 69 71 73 58: 150 type=148 (RBDIHS) 70 69 71 74 58: 151 type=149 (RBDIHS) 89 69 71 72 58: 152 type=149 (RBDIHS) 89 69 71 73 58: 153 type=150 (RBDIHS) 67 69 89 91 58: 154 type=151 (RBDIHS) 71 69 89 91 58: 155 type=148 (RBDIHS) 69 71 74 75 58: 156 type=148 (RBDIHS) 69 71 74 76 58: 157 type=152 (RBDIHS) 69 71 74 77 58: 158 type=148 (RBDIHS) 72 71 74 75 58: 159 type=148 (RBDIHS) 72 71 74 76 58: 160 type=148 (RBDIHS) 72 71 74 77 58: 161 type=148 (RBDIHS) 73 71 74 75 58: 162 type=148 (RBDIHS) 73 71 74 76 58: 163 type=148 (RBDIHS) 73 71 74 77 58: 164 type=148 (RBDIHS) 71 74 77 78 58: 165 type=148 (RBDIHS) 71 74 77 79 58: 166 type=153 (RBDIHS) 71 74 77 80 58: 167 type=148 (RBDIHS) 75 74 77 78 58: 168 type=148 (RBDIHS) 75 74 77 79 58: 169 type=168 (RBDIHS) 75 74 77 80 58: 170 type=148 (RBDIHS) 76 74 77 78 58: 171 type=148 (RBDIHS) 76 74 77 79 58: 172 type=168 (RBDIHS) 76 74 77 80 58: 173 type=169 (RBDIHS) 74 77 80 81 58: 174 type=170 (RBDIHS) 74 77 80 82 58: 175 type=171 (RBDIHS) 78 77 80 82 58: 176 type=171 (RBDIHS) 79 77 80 82 58: 177 type=172 (RBDIHS) 77 80 82 83 58: 178 type=172 (RBDIHS) 77 80 82 86 58: 179 type=173 (RBDIHS) 81 80 82 83 58: 180 type=173 (RBDIHS) 81 80 82 86 58: 181 type=173 (RBDIHS) 80 82 83 84 58: 182 type=173 (RBDIHS) 80 82 83 85 58: 183 type=173 (RBDIHS) 86 82 83 84 58: 184 type=173 (RBDIHS) 86 82 83 85 58: 185 type=173 (RBDIHS) 80 82 86 87 58: 186 type=173 (RBDIHS) 80 82 86 88 58: 187 type=173 (RBDIHS) 83 82 86 87 58: 188 type=173 (RBDIHS) 83 82 86 88 58: 189 type=155 (RBDIHS) 69 89 91 92 58: 190 type=156 (RBDIHS) 69 89 91 93 58: 191 type=155 (RBDIHS) 90 89 91 92 58: 192 type=157 (RBDIHS) 90 89 91 93 58: 193 type=158 (RBDIHS) 89 91 93 95 58: 194 type=159 (RBDIHS) 89 91 93 100 58: 195 type=174 (RBDIHS) 91 93 95 98 58: 196 type=175 (RBDIHS) 100 93 95 98 58: 197 type=147 (RBDIHS) 91 93 95 96 58: 198 type=147 (RBDIHS) 91 93 95 97 58: 199 type=148 (RBDIHS) 94 93 95 96 58: 200 type=148 (RBDIHS) 94 93 95 97 58: 201 type=176 (RBDIHS) 94 93 95 98 58: 202 type=149 (RBDIHS) 100 93 95 96 58: 203 type=149 (RBDIHS) 100 93 95 97 58: 204 type=150 (RBDIHS) 91 93 100 102 58: 205 type=151 (RBDIHS) 95 93 100 102 58: 206 type=177 (RBDIHS) 93 95 98 99 58: 207 type=178 (RBDIHS) 96 95 98 99 58: 208 type=178 (RBDIHS) 97 95 98 99 58: 209 type=155 (RBDIHS) 93 100 102 103 58: 210 type=156 (RBDIHS) 93 100 102 104 58: 211 type=155 (RBDIHS) 101 100 102 103 58: 212 type=157 (RBDIHS) 101 100 102 104 58: 213 type=158 (RBDIHS) 100 102 104 106 58: 214 type=159 (RBDIHS) 100 102 104 115 58: 215 type=179 (RBDIHS) 102 104 106 109 58: 216 type=180 (RBDIHS) 115 104 106 109 58: 217 type=147 (RBDIHS) 102 104 106 107 58: 218 type=147 (RBDIHS) 102 104 106 108 58: 219 type=148 (RBDIHS) 105 104 106 107 58: 220 type=148 (RBDIHS) 105 104 106 108 58: 221 type=148 (RBDIHS) 105 104 106 109 58: 222 type=149 (RBDIHS) 115 104 106 107 58: 223 type=149 (RBDIHS) 115 104 106 108 58: 224 type=150 (RBDIHS) 102 104 115 117 58: 225 type=151 (RBDIHS) 106 104 115 117 58: 226 type=148 (RBDIHS) 104 106 109 110 58: 227 type=148 (RBDIHS) 104 106 109 111 58: 228 type=181 (RBDIHS) 104 106 109 112 58: 229 type=148 (RBDIHS) 107 106 109 110 58: 230 type=148 (RBDIHS) 107 106 109 111 58: 231 type=182 (RBDIHS) 107 106 109 112 58: 232 type=148 (RBDIHS) 108 106 109 110 58: 233 type=148 (RBDIHS) 108 106 109 111 58: 234 type=182 (RBDIHS) 108 106 109 112 58: 235 type=183 (RBDIHS) 106 109 112 113 58: 236 type=183 (RBDIHS) 106 109 112 114 58: 237 type=155 (RBDIHS) 104 115 117 118 58: 238 type=156 (RBDIHS) 104 115 117 119 58: 239 type=155 (RBDIHS) 116 115 117 118 58: 240 type=157 (RBDIHS) 116 115 117 119 58: 241 type=158 (RBDIHS) 115 117 119 121 58: 242 type=159 (RBDIHS) 115 117 119 134 58: 243 type=184 (RBDIHS) 117 119 121 124 58: 244 type=185 (RBDIHS) 134 119 121 124 58: 245 type=147 (RBDIHS) 117 119 121 122 58: 246 type=147 (RBDIHS) 117 119 121 123 58: 247 type=148 (RBDIHS) 120 119 121 122 58: 248 type=148 (RBDIHS) 120 119 121 123 58: 249 type=148 (RBDIHS) 120 119 121 124 58: 250 type=149 (RBDIHS) 134 119 121 122 58: 251 type=149 (RBDIHS) 134 119 121 123 58: 252 type=150 (RBDIHS) 117 119 134 136 58: 253 type=151 (RBDIHS) 121 119 134 136 58: 254 type=148 (RBDIHS) 119 121 124 125 58: 255 type=152 (RBDIHS) 119 121 124 126 58: 256 type=152 (RBDIHS) 119 121 124 130 58: 257 type=148 (RBDIHS) 122 121 124 125 58: 258 type=148 (RBDIHS) 122 121 124 126 58: 259 type=148 (RBDIHS) 122 121 124 130 58: 260 type=148 (RBDIHS) 123 121 124 125 58: 261 type=148 (RBDIHS) 123 121 124 126 58: 262 type=148 (RBDIHS) 123 121 124 130 58: 263 type=148 (RBDIHS) 121 124 126 127 58: 264 type=148 (RBDIHS) 121 124 126 128 58: 265 type=148 (RBDIHS) 121 124 126 129 58: 266 type=148 (RBDIHS) 125 124 126 127 58: 267 type=148 (RBDIHS) 125 124 126 128 58: 268 type=148 (RBDIHS) 125 124 126 129 58: 269 type=148 (RBDIHS) 130 124 126 127 58: 270 type=148 (RBDIHS) 130 124 126 128 58: 271 type=148 (RBDIHS) 130 124 126 129 58: 272 type=148 (RBDIHS) 121 124 130 131 58: 273 type=148 (RBDIHS) 121 124 130 132 58: 274 type=148 (RBDIHS) 121 124 130 133 58: 275 type=148 (RBDIHS) 125 124 130 131 58: 276 type=148 (RBDIHS) 125 124 130 132 58: 277 type=148 (RBDIHS) 125 124 130 133 58: 278 type=148 (RBDIHS) 126 124 130 131 58: 279 type=148 (RBDIHS) 126 124 130 132 58: 280 type=148 (RBDIHS) 126 124 130 133 58: 281 type=155 (RBDIHS) 119 134 136 137 58: 282 type=156 (RBDIHS) 119 134 136 138 58: 283 type=155 (RBDIHS) 135 134 136 137 58: 284 type=157 (RBDIHS) 135 134 136 138 58: 285 type=158 (RBDIHS) 134 136 138 140 58: 286 type=159 (RBDIHS) 134 136 138 144 58: 287 type=147 (RBDIHS) 136 138 140 141 58: 288 type=147 (RBDIHS) 136 138 140 142 58: 289 type=147 (RBDIHS) 136 138 140 143 58: 290 type=148 (RBDIHS) 139 138 140 141 58: 291 type=148 (RBDIHS) 139 138 140 142 58: 292 type=148 (RBDIHS) 139 138 140 143 58: 293 type=149 (RBDIHS) 144 138 140 141 58: 294 type=149 (RBDIHS) 144 138 140 142 58: 295 type=149 (RBDIHS) 144 138 140 143 58: 296 type=150 (RBDIHS) 136 138 144 146 58: 297 type=151 (RBDIHS) 140 138 144 146 58: 298 type=155 (RBDIHS) 138 144 146 147 58: 299 type=156 (RBDIHS) 138 144 146 148 58: 300 type=155 (RBDIHS) 145 144 146 147 58: 301 type=157 (RBDIHS) 145 144 146 148 58: 302 type=158 (RBDIHS) 144 146 148 150 58: 303 type=159 (RBDIHS) 144 146 148 154 58: 304 type=147 (RBDIHS) 146 148 150 151 58: 305 type=147 (RBDIHS) 146 148 150 152 58: 306 type=147 (RBDIHS) 146 148 150 153 58: 307 type=148 (RBDIHS) 149 148 150 151 58: 308 type=148 (RBDIHS) 149 148 150 152 58: 309 type=148 (RBDIHS) 149 148 150 153 58: 310 type=149 (RBDIHS) 154 148 150 151 58: 311 type=149 (RBDIHS) 154 148 150 152 58: 312 type=149 (RBDIHS) 154 148 150 153 58: Restr. Dih.: 58: nr: 0 58: CBT Dih.: 58: nr: 0 58: Fourier Dih.: 58: nr: 0 58: Improper Dih.: 58: nr: 0 58: Per. Imp. Dih.: 58: nr: 0 58: Tab. Dih.: 58: nr: 0 58: CMAP Dih.: 58: nr: 0 58: GB 1-2 Pol.: 58: nr: 0 58: GB 1-3 Pol.: 58: nr: 0 58: GB 1-4 Pol.: 58: nr: 0 58: GB Polariz.: 58: nr: 0 58: Nonpolar Sol.: 58: nr: 0 58: LJ-14: 58: nr: 1197 58: iatoms: 58: 0 type=186 (LJ14) 0 7 58: 1 type=186 (LJ14) 0 8 58: 2 type=187 (LJ14) 0 9 58: 3 type=188 (LJ14) 0 23 58: 4 type=189 (LJ14) 0 24 58: 5 type=190 (LJ14) 1 5 58: 6 type=190 (LJ14) 1 6 58: 7 type=190 (LJ14) 1 22 58: 8 type=190 (LJ14) 2 5 58: 9 type=190 (LJ14) 2 6 58: 10 type=190 (LJ14) 2 22 58: 11 type=190 (LJ14) 3 5 58: 12 type=190 (LJ14) 3 6 58: 13 type=190 (LJ14) 3 22 58: 14 type=191 (LJ14) 4 10 58: 15 type=191 (LJ14) 4 11 58: 16 type=192 (LJ14) 4 12 58: 17 type=190 (LJ14) 4 25 58: 18 type=192 (LJ14) 4 26 58: 19 type=193 (LJ14) 5 7 58: 20 type=193 (LJ14) 5 8 58: 21 type=191 (LJ14) 5 9 58: 22 type=194 (LJ14) 5 23 58: 23 type=186 (LJ14) 5 24 58: 24 type=191 (LJ14) 6 13 58: 25 type=191 (LJ14) 6 14 58: 26 type=192 (LJ14) 6 15 58: 27 type=195 (LJ14) 6 23 58: 28 type=187 (LJ14) 6 24 58: 29 type=193 (LJ14) 7 10 58: 30 type=193 (LJ14) 7 11 58: 31 type=191 (LJ14) 7 12 58: 32 type=196 (LJ14) 7 22 58: 33 type=193 (LJ14) 8 10 58: 34 type=193 (LJ14) 8 11 58: 35 type=191 (LJ14) 8 12 58: 36 type=196 (LJ14) 8 22 58: 37 type=191 (LJ14) 9 16 58: 38 type=191 (LJ14) 9 17 58: 39 type=187 (LJ14) 9 18 58: 40 type=197 (LJ14) 9 22 58: 41 type=193 (LJ14) 10 13 58: 42 type=193 (LJ14) 10 14 58: 43 type=191 (LJ14) 10 15 58: 44 type=193 (LJ14) 11 13 58: 45 type=193 (LJ14) 11 14 58: 46 type=191 (LJ14) 11 15 58: 47 type=190 (LJ14) 12 19 58: 48 type=190 (LJ14) 12 20 58: 49 type=190 (LJ14) 12 21 58: 50 type=193 (LJ14) 13 16 58: 51 type=193 (LJ14) 13 17 58: 52 type=186 (LJ14) 13 18 58: 53 type=193 (LJ14) 14 16 58: 54 type=193 (LJ14) 14 17 58: 55 type=186 (LJ14) 14 18 58: 56 type=190 (LJ14) 16 19 58: 57 type=190 (LJ14) 16 20 58: 58 type=190 (LJ14) 16 21 58: 59 type=190 (LJ14) 17 19 58: 60 type=190 (LJ14) 17 20 58: 61 type=190 (LJ14) 17 21 58: 62 type=196 (LJ14) 22 27 58: 63 type=197 (LJ14) 22 28 58: 64 type=198 (LJ14) 22 38 58: 65 type=190 (LJ14) 23 25 58: 66 type=195 (LJ14) 23 26 58: 67 type=186 (LJ14) 24 29 58: 68 type=187 (LJ14) 24 30 58: 69 type=187 (LJ14) 24 34 58: 70 type=188 (LJ14) 24 39 58: 71 type=189 (LJ14) 24 40 58: 72 type=190 (LJ14) 25 27 58: 73 type=190 (LJ14) 25 28 58: 74 type=190 (LJ14) 25 38 58: 75 type=191 (LJ14) 26 31 58: 76 type=191 (LJ14) 26 32 58: 77 type=191 (LJ14) 26 33 58: 78 type=191 (LJ14) 26 35 58: 79 type=191 (LJ14) 26 36 58: 80 type=191 (LJ14) 26 37 58: 81 type=190 (LJ14) 26 41 58: 82 type=192 (LJ14) 26 42 58: 83 type=193 (LJ14) 27 29 58: 84 type=191 (LJ14) 27 30 58: 85 type=191 (LJ14) 27 34 58: 86 type=194 (LJ14) 27 39 58: 87 type=186 (LJ14) 27 40 58: 88 type=195 (LJ14) 28 39 58: 89 type=187 (LJ14) 28 40 58: 90 type=193 (LJ14) 29 31 58: 91 type=193 (LJ14) 29 32 58: 92 type=193 (LJ14) 29 33 58: 93 type=193 (LJ14) 29 35 58: 94 type=193 (LJ14) 29 36 58: 95 type=193 (LJ14) 29 37 58: 96 type=196 (LJ14) 29 38 58: 97 type=191 (LJ14) 30 35 58: 98 type=191 (LJ14) 30 36 58: 99 type=191 (LJ14) 30 37 58: 100 type=197 (LJ14) 30 38 58: 101 type=191 (LJ14) 31 34 58: 102 type=191 (LJ14) 32 34 58: 103 type=191 (LJ14) 33 34 58: 104 type=197 (LJ14) 34 38 58: 105 type=196 (LJ14) 38 43 58: 106 type=197 (LJ14) 38 44 58: 107 type=198 (LJ14) 38 58 58: 108 type=190 (LJ14) 39 41 58: 109 type=195 (LJ14) 39 42 58: 110 type=186 (LJ14) 40 45 58: 111 type=186 (LJ14) 40 46 58: 112 type=199 (LJ14) 40 47 58: 113 type=188 (LJ14) 40 59 58: 114 type=189 (LJ14) 40 60 58: 115 type=190 (LJ14) 41 43 58: 116 type=190 (LJ14) 41 44 58: 117 type=190 (LJ14) 41 58 58: 118 type=200 (LJ14) 42 48 58: 119 type=200 (LJ14) 42 50 58: 120 type=190 (LJ14) 42 61 58: 121 type=192 (LJ14) 42 62 58: 122 type=193 (LJ14) 43 45 58: 123 type=193 (LJ14) 43 46 58: 124 type=201 (LJ14) 43 47 58: 125 type=194 (LJ14) 43 59 58: 126 type=186 (LJ14) 43 60 58: 127 type=202 (LJ14) 44 49 58: 128 type=202 (LJ14) 44 51 58: 129 type=200 (LJ14) 44 52 58: 130 type=200 (LJ14) 44 54 58: 131 type=195 (LJ14) 44 59 58: 132 type=187 (LJ14) 44 60 58: 133 type=201 (LJ14) 45 48 58: 134 type=201 (LJ14) 45 50 58: 135 type=196 (LJ14) 45 58 58: 136 type=201 (LJ14) 46 48 58: 137 type=201 (LJ14) 46 50 58: 138 type=196 (LJ14) 46 58 58: 139 type=203 (LJ14) 47 53 58: 140 type=203 (LJ14) 47 55 58: 141 type=204 (LJ14) 47 56 58: 142 type=205 (LJ14) 47 58 58: 143 type=203 (LJ14) 48 51 58: 144 type=204 (LJ14) 48 54 58: 145 type=203 (LJ14) 48 57 58: 146 type=203 (LJ14) 49 50 58: 147 type=206 (LJ14) 49 53 58: 148 type=203 (LJ14) 49 56 58: 149 type=204 (LJ14) 50 52 58: 150 type=203 (LJ14) 50 57 58: 151 type=206 (LJ14) 51 55 58: 152 type=203 (LJ14) 51 56 58: 153 type=203 (LJ14) 52 55 58: 154 type=203 (LJ14) 53 54 58: 155 type=206 (LJ14) 53 57 58: 156 type=206 (LJ14) 55 57 58: 157 type=196 (LJ14) 58 63 58: 158 type=196 (LJ14) 58 64 58: 159 type=198 (LJ14) 58 65 58: 160 type=190 (LJ14) 59 61 58: 161 type=195 (LJ14) 59 62 58: 162 type=188 (LJ14) 60 66 58: 163 type=189 (LJ14) 60 67 58: 164 type=190 (LJ14) 61 63 58: 165 type=190 (LJ14) 61 64 58: 166 type=190 (LJ14) 61 65 58: 167 type=190 (LJ14) 62 68 58: 168 type=192 (LJ14) 62 69 58: 169 type=194 (LJ14) 63 66 58: 170 type=186 (LJ14) 63 67 58: 171 type=194 (LJ14) 64 66 58: 172 type=186 (LJ14) 64 67 58: 173 type=196 (LJ14) 65 70 58: 174 type=197 (LJ14) 65 71 58: 175 type=198 (LJ14) 65 89 58: 176 type=190 (LJ14) 66 68 58: 177 type=195 (LJ14) 66 69 58: 178 type=186 (LJ14) 67 72 58: 179 type=186 (LJ14) 67 73 58: 180 type=187 (LJ14) 67 74 58: 181 type=188 (LJ14) 67 90 58: 182 type=189 (LJ14) 67 91 58: 183 type=190 (LJ14) 68 70 58: 184 type=190 (LJ14) 68 71 58: 185 type=190 (LJ14) 68 89 58: 186 type=191 (LJ14) 69 75 58: 187 type=191 (LJ14) 69 76 58: 188 type=192 (LJ14) 69 77 58: 189 type=190 (LJ14) 69 92 58: 190 type=192 (LJ14) 69 93 58: 191 type=193 (LJ14) 70 72 58: 192 type=193 (LJ14) 70 73 58: 193 type=191 (LJ14) 70 74 58: 194 type=194 (LJ14) 70 90 58: 195 type=186 (LJ14) 70 91 58: 196 type=191 (LJ14) 71 78 58: 197 type=191 (LJ14) 71 79 58: 198 type=187 (LJ14) 71 80 58: 199 type=195 (LJ14) 71 90 58: 200 type=187 (LJ14) 71 91 58: 201 type=193 (LJ14) 72 75 58: 202 type=193 (LJ14) 72 76 58: 203 type=191 (LJ14) 72 77 58: 204 type=196 (LJ14) 72 89 58: 205 type=193 (LJ14) 73 75 58: 206 type=193 (LJ14) 73 76 58: 207 type=191 (LJ14) 73 77 58: 208 type=196 (LJ14) 73 89 58: 209 type=190 (LJ14) 74 81 58: 210 type=207 (LJ14) 74 82 58: 211 type=197 (LJ14) 74 89 58: 212 type=193 (LJ14) 75 78 58: 213 type=193 (LJ14) 75 79 58: 214 type=186 (LJ14) 75 80 58: 215 type=193 (LJ14) 76 78 58: 216 type=193 (LJ14) 76 79 58: 217 type=186 (LJ14) 76 80 58: 218 type=187 (LJ14) 77 83 58: 219 type=187 (LJ14) 77 86 58: 220 type=190 (LJ14) 78 81 58: 221 type=208 (LJ14) 78 82 58: 222 type=190 (LJ14) 79 81 58: 223 type=208 (LJ14) 79 82 58: 224 type=190 (LJ14) 80 84 58: 225 type=190 (LJ14) 80 85 58: 226 type=190 (LJ14) 80 87 58: 227 type=190 (LJ14) 80 88 58: 228 type=190 (LJ14) 81 83 58: 229 type=190 (LJ14) 81 86 58: 230 type=190 (LJ14) 83 87 58: 231 type=190 (LJ14) 83 88 58: 232 type=190 (LJ14) 84 86 58: 233 type=190 (LJ14) 85 86 58: 234 type=196 (LJ14) 89 94 58: 235 type=197 (LJ14) 89 95 58: 236 type=198 (LJ14) 89 100 58: 237 type=190 (LJ14) 90 92 58: 238 type=195 (LJ14) 90 93 58: 239 type=186 (LJ14) 91 96 58: 240 type=186 (LJ14) 91 97 58: 241 type=209 (LJ14) 91 98 58: 242 type=188 (LJ14) 91 101 58: 243 type=189 (LJ14) 91 102 58: 244 type=190 (LJ14) 92 94 58: 245 type=190 (LJ14) 92 95 58: 246 type=190 (LJ14) 92 100 58: 247 type=190 (LJ14) 93 99 58: 248 type=190 (LJ14) 93 103 58: 249 type=192 (LJ14) 93 104 58: 250 type=193 (LJ14) 94 96 58: 251 type=193 (LJ14) 94 97 58: 252 type=210 (LJ14) 94 98 58: 253 type=194 (LJ14) 94 101 58: 254 type=186 (LJ14) 94 102 58: 255 type=195 (LJ14) 95 101 58: 256 type=187 (LJ14) 95 102 58: 257 type=190 (LJ14) 96 99 58: 258 type=196 (LJ14) 96 100 58: 259 type=190 (LJ14) 97 99 58: 260 type=196 (LJ14) 97 100 58: 261 type=211 (LJ14) 98 100 58: 262 type=196 (LJ14) 100 105 58: 263 type=197 (LJ14) 100 106 58: 264 type=198 (LJ14) 100 115 58: 265 type=190 (LJ14) 101 103 58: 266 type=195 (LJ14) 101 104 58: 267 type=186 (LJ14) 102 107 58: 268 type=186 (LJ14) 102 108 58: 269 type=187 (LJ14) 102 109 58: 270 type=188 (LJ14) 102 116 58: 271 type=189 (LJ14) 102 117 58: 272 type=190 (LJ14) 103 105 58: 273 type=190 (LJ14) 103 106 58: 274 type=190 (LJ14) 103 115 58: 275 type=191 (LJ14) 104 110 58: 276 type=191 (LJ14) 104 111 58: 277 type=197 (LJ14) 104 112 58: 278 type=190 (LJ14) 104 118 58: 279 type=192 (LJ14) 104 119 58: 280 type=193 (LJ14) 105 107 58: 281 type=193 (LJ14) 105 108 58: 282 type=191 (LJ14) 105 109 58: 283 type=194 (LJ14) 105 116 58: 284 type=186 (LJ14) 105 117 58: 285 type=195 (LJ14) 106 113 58: 286 type=195 (LJ14) 106 114 58: 287 type=195 (LJ14) 106 116 58: 288 type=187 (LJ14) 106 117 58: 289 type=193 (LJ14) 107 110 58: 290 type=193 (LJ14) 107 111 58: 291 type=196 (LJ14) 107 112 58: 292 type=196 (LJ14) 107 115 58: 293 type=193 (LJ14) 108 110 58: 294 type=193 (LJ14) 108 111 58: 295 type=196 (LJ14) 108 112 58: 296 type=196 (LJ14) 108 115 58: 297 type=197 (LJ14) 109 115 58: 298 type=194 (LJ14) 110 113 58: 299 type=194 (LJ14) 110 114 58: 300 type=194 (LJ14) 111 113 58: 301 type=194 (LJ14) 111 114 58: 302 type=196 (LJ14) 115 120 58: 303 type=197 (LJ14) 115 121 58: 304 type=198 (LJ14) 115 134 58: 305 type=190 (LJ14) 116 118 58: 306 type=195 (LJ14) 116 119 58: 307 type=186 (LJ14) 117 122 58: 308 type=186 (LJ14) 117 123 58: 309 type=187 (LJ14) 117 124 58: 310 type=188 (LJ14) 117 135 58: 311 type=189 (LJ14) 117 136 58: 312 type=190 (LJ14) 118 120 58: 313 type=190 (LJ14) 118 121 58: 314 type=190 (LJ14) 118 134 58: 315 type=191 (LJ14) 119 125 58: 316 type=192 (LJ14) 119 126 58: 317 type=192 (LJ14) 119 130 58: 318 type=190 (LJ14) 119 137 58: 319 type=192 (LJ14) 119 138 58: 320 type=193 (LJ14) 120 122 58: 321 type=193 (LJ14) 120 123 58: 322 type=191 (LJ14) 120 124 58: 323 type=194 (LJ14) 120 135 58: 324 type=186 (LJ14) 120 136 58: 325 type=191 (LJ14) 121 127 58: 326 type=191 (LJ14) 121 128 58: 327 type=191 (LJ14) 121 129 58: 328 type=191 (LJ14) 121 131 58: 329 type=191 (LJ14) 121 132 58: 330 type=191 (LJ14) 121 133 58: 331 type=195 (LJ14) 121 135 58: 332 type=187 (LJ14) 121 136 58: 333 type=193 (LJ14) 122 125 58: 334 type=191 (LJ14) 122 126 58: 335 type=191 (LJ14) 122 130 58: 336 type=196 (LJ14) 122 134 58: 337 type=193 (LJ14) 123 125 58: 338 type=191 (LJ14) 123 126 58: 339 type=191 (LJ14) 123 130 58: 340 type=196 (LJ14) 123 134 58: 341 type=197 (LJ14) 124 134 58: 342 type=193 (LJ14) 125 127 58: 343 type=193 (LJ14) 125 128 58: 344 type=193 (LJ14) 125 129 58: 345 type=193 (LJ14) 125 131 58: 346 type=193 (LJ14) 125 132 58: 347 type=193 (LJ14) 125 133 58: 348 type=191 (LJ14) 126 131 58: 349 type=191 (LJ14) 126 132 58: 350 type=191 (LJ14) 126 133 58: 351 type=191 (LJ14) 127 130 58: 352 type=191 (LJ14) 128 130 58: 353 type=191 (LJ14) 129 130 58: 354 type=196 (LJ14) 134 139 58: 355 type=197 (LJ14) 134 140 58: 356 type=198 (LJ14) 134 144 58: 357 type=190 (LJ14) 135 137 58: 358 type=195 (LJ14) 135 138 58: 359 type=186 (LJ14) 136 141 58: 360 type=186 (LJ14) 136 142 58: 361 type=186 (LJ14) 136 143 58: 362 type=188 (LJ14) 136 145 58: 363 type=189 (LJ14) 136 146 58: 364 type=190 (LJ14) 137 139 58: 365 type=190 (LJ14) 137 140 58: 366 type=190 (LJ14) 137 144 58: 367 type=190 (LJ14) 138 147 58: 368 type=192 (LJ14) 138 148 58: 369 type=193 (LJ14) 139 141 58: 370 type=193 (LJ14) 139 142 58: 371 type=193 (LJ14) 139 143 58: 372 type=194 (LJ14) 139 145 58: 373 type=186 (LJ14) 139 146 58: 374 type=195 (LJ14) 140 145 58: 375 type=187 (LJ14) 140 146 58: 376 type=196 (LJ14) 141 144 58: 377 type=196 (LJ14) 142 144 58: 378 type=196 (LJ14) 143 144 58: 379 type=196 (LJ14) 144 149 58: 380 type=197 (LJ14) 144 150 58: 381 type=198 (LJ14) 144 154 58: 382 type=190 (LJ14) 145 147 58: 383 type=195 (LJ14) 145 148 58: 384 type=186 (LJ14) 146 151 58: 385 type=186 (LJ14) 146 152 58: 386 type=186 (LJ14) 146 153 58: 387 type=188 (LJ14) 146 155 58: 388 type=190 (LJ14) 147 149 58: 389 type=190 (LJ14) 147 150 58: 390 type=190 (LJ14) 147 154 58: 391 type=193 (LJ14) 149 151 58: 392 type=193 (LJ14) 149 152 58: 393 type=193 (LJ14) 149 153 58: 394 type=194 (LJ14) 149 155 58: 395 type=195 (LJ14) 150 155 58: 396 type=196 (LJ14) 151 154 58: 397 type=196 (LJ14) 152 154 58: 398 type=196 (LJ14) 153 154 58: Coulomb-14: 58: nr: 0 58: LJC-14 q: 58: nr: 0 58: LJC Pairs NB: 58: nr: 0 58: LJ (SR): 58: nr: 0 58: Buck.ham (SR): 58: nr: 0 58: LJ: 58: nr: 0 58: B.ham: 58: nr: 0 58: Disper. corr.: 58: nr: 0 58: Coulomb (SR): 58: nr: 0 58: Coul: 58: nr: 0 58: RF excl.: 58: nr: 0 58: Coul. recip.: 58: nr: 0 58: LJ recip.: 58: nr: 0 58: DPD: 58: nr: 0 58: Polarization: 58: nr: 0 58: Water Pol.: 58: nr: 0 58: Thole Pol.: 58: nr: 0 58: Anharm. Pol.: 58: nr: 0 58: Position Rest.: 58: nr: 0 58: Flat-b. P-R.: 58: nr: 0 58: Dis. Rest.: 58: nr: 0 58: D.R.Viol. (nm): 58: nr: 0 58: Orient. Rest.: 58: nr: 0 58: Ori. R. RMSD: 58: nr: 0 58: Angle Rest.: 58: nr: 0 58: Angle Rest. Z: 58: nr: 0 58: Dih. Rest.: 58: nr: 0 58: Dih. Rest. Vi.: 58: nr: 0 58: Constraint: 58: nr: 0 58: Constr. No Co.: 58: nr: 0 58: Settle: 58: nr: 0 58: Virtual site 1: 58: nr: 0 58: Virtual site 2: 58: nr: 0 58: Virt. site 2fd: 58: nr: 0 58: Virtual site 3: 58: nr: 0 58: Virt. site 3fd: 58: nr: 0 58: Vir. site 3fad: 58: nr: 0 58: Vir. site 3out: 58: nr: 0 58: Virt. site 4fd: 58: nr: 0 58: Vir. site 4fdn: 58: nr: 0 58: Virtual site N: 58: nr: 0 58: COM Pull En.: 58: nr: 0 58: Dens. fitting: 58: nr: 0 58: Quantum En.: 58: nr: 0 58: Potential: 58: nr: 0 58: Kinetic En.: 58: nr: 0 58: Total Energy: 58: nr: 0 58: Conserved En.: 58: nr: 0 58: Temperature: 58: nr: 0 58: Vir. Temp.: 58: nr: 0 58: Pres. DC: 58: nr: 0 58: Pressure: 58: nr: 0 58: dH/dl constr.: 58: nr: 0 58: dVremain/dl: 58: nr: 0 58: dEkin/dl: 58: nr: 0 58: dVcoul/dl: 58: nr: 0 58: dVvdw/dl: 58: nr: 0 58: dVbonded/dl: 58: nr: 0 58: dVrestraint/dl: 58: nr: 0 58: dVtemp/dl: 58: nr: 0 58: grp[T-Coupling ] nr=1, name=[ rest] 58: grp[Energy Mon. ] nr=1, name=[ rest] 58: grp[Acc. not used] nr=1, name=[ rest] 58: grp[Freeze ] nr=1, name=[ rest] 58: grp[User1 ] nr=1, name=[ rest] 58: grp[User2 ] nr=1, name=[ rest] 58: grp[VCM ] nr=1, name=[ rest] 58: grp[Compressed X] nr=1, name=[ rest] 58: grp[Or. Res. Fit] nr=1, name=[ rest] 58: grp[QMMM ] nr=1, name=[ rest] 58: grpname (11): 58: grpname[0]={name="System"} 58: grpname[1]={name="Protein"} 58: grpname[2]={name="Protein-H"} 58: grpname[3]={name="C-alpha"} 58: grpname[4]={name="Backbone"} 58: grpname[5]={name="MainChain"} 58: grpname[6]={name="MainChain+Cb"} 58: grpname[7]={name="MainChain+H"} 58: grpname[8]={name="SideChain"} 58: grpname[9]={name="SideChain-H"} 58: grpname[10]={name="rest"} 58: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 58: allocated 0 0 0 0 0 0 0 0 0 0 58: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 58: box (3x3): 58: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 58: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 58: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 58: box_rel (3x3): 58: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv (3x3): 58: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev (3x3): 58: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev (3x3): 58: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev (3x3): 58: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: nosehoover_xi: not available 58: x (156x3): 58: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 58: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 58: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 58: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 58: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 58: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 58: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 58: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 58: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 58: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 58: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 58: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 58: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 58: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 58: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 58: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 58: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 58: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 58: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 58: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 58: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 58: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 58: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 58: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 58: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 58: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 58: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 58: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 58: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 58: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 58: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 58: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 58: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 58: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 58: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 58: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 58: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 58: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 58: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 58: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 58: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 58: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 58: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 58: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 58: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 58: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 58: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 58: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 58: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 58: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 58: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 58: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 58: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 58: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 58: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 58: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 58: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 58: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 58: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 58: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 58: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 58: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 58: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 58: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 58: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 58: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 58: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 58: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 58: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 58: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 58: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 58: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 58: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 58: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 58: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 58: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 58: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 58: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 58: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 58: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 58: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 58: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 58: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 58: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 58: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 58: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 58: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 58: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 58: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 58: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 58: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 58: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 58: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 58: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 58: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 58: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 58: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 58: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 58: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 58: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 58: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 58: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 58: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 58: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 58: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 58: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 58: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 58: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 58: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 58: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 58: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 58: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 58: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 58: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 58: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 58: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 58: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 58: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 58: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 58: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 58: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 58: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 58: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 58: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 58: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 58: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 58: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 58: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 58: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 58: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 58: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 58: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 58: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 58: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 58: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 58: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 58: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 58: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 58: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 58: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 58: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 58: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 58: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 58: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 58: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 58: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 58: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 58: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 58: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 58: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 58: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 58: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 58: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 58: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 58: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 58: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 58: v (156x3): 58: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 58: Group statistics 58: T-Coupling : 156 (total 156 atoms) 58: Energy Mon. : 156 (total 156 atoms) 58: Acc. not used: 156 (total 156 atoms) 58: Freeze : 156 (total 156 atoms) 58: User1 : 156 (total 156 atoms) 58: User2 : 156 (total 156 atoms) 58: VCM : 156 (total 156 atoms) 58: Compressed X: 156 (total 156 atoms) 58: Or. Res. Fit: 156 (total 156 atoms) 58: QMMM : 156 (total 156 atoms) 58: [ OK ] DumpTest.WorksWithTpr (45 ms) 58: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 58: [----------] 2 tests from DumpTest (62 ms total) 58: 58: [----------] 3 tests from HelpwritingTest 58: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 58: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 58: [ RUN ] HelpwritingTest.DumpWritesHelp 58: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 58: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 58: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 58: [----------] 3 tests from HelpwritingTest (0 ms total) 58: 58: [----------] 7 tests from GmxMakeNdx 58: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 16 Protein residues 58: Analysing Protein... 58: 58: 0 System : 256 atoms 58: 1 Protein : 256 atoms 58: 2 Protein-H : 139 atoms 58: 3 C-alpha : 16 atoms 58: 4 Backbone : 48 atoms 58: 5 MainChain : 63 atoms 58: 6 MainChain+Cb : 78 atoms 58: 7 MainChain+H : 81 atoms 58: 8 SideChain : 175 atoms 58: 9 SideChain-H : 76 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (15 ms) 58: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 58: Going to read 1 old index file(s) 58: Deducing 22 atoms in the system from indices in the index file 58: 58: 0 System : 22 atoms 58: 1 Protein : 22 atoms 58: 2 Protein-H : 10 atoms 58: 3 C-alpha : 1 atoms 58: 4 Backbone : 5 atoms 58: 5 MainChain : 7 atoms 58: 6 MainChain+Cb : 8 atoms 58: 7 MainChain+H : 9 atoms 58: 8 SideChain : 13 atoms 58: 9 SideChain-H : 3 atoms 58: 10 CA : 1 atoms 58: 11 C_&_r_1 : 1 atoms 58: 12 C_&_r_2 : 1 atoms 58: 13 N_&_r_2 : 1 atoms 58: 14 N_&_r_3 : 1 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Copied index group 1 'Protein' 58: Copied index group 2 'Protein-H' 58: Merged two groups with OR: 22 10 -> 22 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 58: [ RUN ] GmxMakeNdx.HandlesNotProtein 58: Going to read 1 old index file(s) 58: Deducing 6 atoms in the system from indices in the index file 58: 58: 0 System : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 58: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 58: Going to read 1 old index file(s) 58: Deducing 22 atoms in the system from indices in the index file 58: 58: 0 System : 22 atoms 58: 1 Protein : 22 atoms 58: 2 Protein-H : 10 atoms 58: 3 C-alpha : 1 atoms 58: 4 Backbone : 5 atoms 58: 5 MainChain : 7 atoms 58: 6 MainChain+Cb : 8 atoms 58: 7 MainChain+H : 9 atoms 58: 8 SideChain : 13 atoms 58: 9 SideChain-H : 3 atoms 58: 10 CA : 1 atoms 58: 11 C_&_r_1 : 1 atoms 58: 12 C_&_r_2 : 1 atoms 58: 13 N_&_r_2 : 1 atoms 58: 14 N_&_r_3 : 1 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Copied index group 4 'Backbone' 58: Copied index group 8 'SideChain' 58: Merged two groups with AND: 5 13 -> 0 58: Group is empty 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (25 ms) 58: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 58: Going to read 1 old index file(s) 58: Deducing 6 atoms in the system from indices in the index file 58: 58: 0 System : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Removed group 0 'System' 58: 58: > 58: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 58: [ RUN ] GmxMakeNdx.Splitres 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 2 Water residues 58: 58: 0 System : 6 atoms 58: 1 Water : 6 atoms 58: 2 SOL : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Splitting group 1 'Water' into residues 58: 58: > 58: [ OK ] GmxMakeNdx.Splitres (0 ms) 58: [ RUN ] GmxMakeNdx.Splitat 58: 58: Reading structure file 58: Going to read 0 old index file(s) 58: Analysing residue names: 58: There are: 2 Water residues 58: 58: 0 System : 6 atoms 58: 1 Water : 6 atoms 58: 2 SOL : 6 atoms 58: 58: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 58: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 58: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 58: 'r': residue 'res' nr 'chain' char 58: "name": group 'case': case sensitive 'q': save and quit 58: 'ri': residue index 58: 58: > 58: Splitting group 1 'Water' into atoms 58: 58: > 58: [ OK ] GmxMakeNdx.Splitat (0 ms) 58: [----------] 7 tests from GmxMakeNdx (43 ms total) 58: 58: [----------] 4 tests from ReportMethodsTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Setting the LD random seed to -1982334090 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 58: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 58: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 58: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 58: [ RUN ] ReportMethodsTest.WritesCorrectInformation 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 58: [ RUN ] ReportMethodsTest.ToolEndToEndTest 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: section: Methods 58: subsection: Simulation system 58: A system of 1 molecules (156 atoms) was simulated. 58: 58: subsection: Simulation settings 58: A total of 0 ns were simulated with a time step of 1 fs. 58: Neighbor searching was performed every 10 steps. 58: The Cut-off algorithm was used for electrostatic interactions. 58: with a cut-off of 1 nm. 58: A single cut-off of 1.1 nm was used for Van der Waals interactions. 58: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 58: [----------] 4 tests from ReportMethodsTest (0 ms total) 58: 58: [----------] 4 tests from ConvertTprTest 58: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting the LD random seed to 1765013431 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: Extending remaining runtime by 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: Extending remaining runtime by 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 200000 58: Runtime for the run 200 ps 58: Run end step 200000 58: Run end time 200 ps 58: 58: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (1220 ms) 58: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting the LD random seed to -1210466500 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: Extending remaining runtime to 100 ps 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 100000 58: Runtime for the run 100 ps 58: Run end step 100000 58: Run end time 100 ps 58: 58: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (1192 ms) 58: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting nsteps to 102 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting the LD random seed to -539033819 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: Input file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 0 58: Runtime for the run 0 ps 58: Run end step 0 58: Run end time 0 ps 58: 58: 58: Output file: 58: Run start step 0 58: Run start time 0 ps 58: Step to be made during run 102 58: Runtime for the run 0.102 ps 58: Run end step 102 58: Run end time 0.102 ps 58: 58: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (1187 ms) 58: [ RUN ] ConvertTprTest.generateVelocitiesTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 58: Setting the LD random seed to -1209073665 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] ConvertTprTest.generateVelocitiesTest (1164 ms) 58: [----------] 4 tests from ConvertTprTest (4764 ms total) 58: 58: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (16 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 58: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 58: Will write trr: Trajectory in portable xdr format 58: Group 0 ( System) has 6 elements 58: Group 1 (FirstWaterMolecule) has 3 elements 58: Group 2 (SecondWaterMolecule) has 3 elements 58: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 58: -> frame 1 time 1.000 58: Last written: frame 1 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: Select group for output 58: Selected 2: 'SecondWaterMolecule' 58: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 58: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (20 ms total) 58: 58: [----------] 30 tests from Works/TrjconvDumpTest 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (16 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (4 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 58: Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 58: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 58: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 58: Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 0 ps 58: -> frame 0 time 0.000 58: Last written: frame 0 time 0.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 58: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 58: Will write trr: Trajectory in portable xdr format 58: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 58: 58: Dumping frame at t= 1 ps 58: -> frame 0 time 1.000 58: Last written: frame 0 time 1.000 58: 58: 58: Note that major changes are planned in future for trjconv, to improve usability and utility. 58: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 58: [----------] 30 tests from Works/TrjconvDumpTest (28 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 62 tests from 7 test suites ran. (7557 ms total) 58: [ PASSED ] 62 tests. 58/87 Test #58: ToolUnitTests ............................. Passed 7.65 sec test 59 Start 59: FileIOTests 59: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/FileIOTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/fileio/tests 59: Test timeout computed to be: 30 59: [==========] Running 413 tests from 15 test suites. 59: [----------] Global test environment set-up. 59: [----------] 4 tests from Checkpoint 59: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 59: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 59: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 59: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 59: [ RUN ] Checkpoint.KvtRoundTripInt64 59: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 59: [ RUN ] Checkpoint.KvtRoundTripReal 59: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 59: [----------] 4 tests from Checkpoint (0 ms total) 59: 59: [----------] 1 test from StructureIOTest 59: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 59: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 59: [----------] 1 test from StructureIOTest (0 ms total) 59: 59: [----------] 2 tests from FileMD5Test 59: [ RUN ] FileMD5Test.CanComputeMD5 59: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 59: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 59: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 59: [----------] 2 tests from FileMD5Test (0 ms total) 59: 59: [----------] 4 tests from FileTypeTest 59: [ RUN ] FileTypeTest.CorrectValueForEmptyString 59: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForNoExtension 59: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 59: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 59: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 59: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 59: [----------] 4 tests from FileTypeTest (0 ms total) 59: 59: [----------] 3 tests from MrcSerializer 59: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 59: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 59: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 59: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 59: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 59: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 59: [----------] 3 tests from MrcSerializer (0 ms total) 59: 59: [----------] 4 tests from MrcDensityMap 59: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 59: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 59: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 59: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 59: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 59: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 59: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 59: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 59: [----------] 4 tests from MrcDensityMap (0 ms total) 59: 59: [----------] 8 tests from MrcDensityMapHeaderTest 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 59: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 59: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 59: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 59: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 59: [ RUN ] MrcDensityMapHeaderTest.IsSane 59: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 59: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 59: 59: [----------] 10 tests from ReadTest 59: [ RUN ] ReadTest.get_eint_ReadsInteger 59: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 59: 59: ERROR 1 [file unknown]: 59: Right hand side '0.8' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 59: [ RUN ] ReadTest.get_eint_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.get_eint64_ReadsInteger 59: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 59: 59: ERROR 1 [file unknown]: 59: Right hand side '0.8' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 59: [ RUN ] ReadTest.get_eint64_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not an 59: integer value 59: 59: 59: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.get_ereal_ReadsInteger 59: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 59: [ RUN ] ReadTest.get_ereal_ReadsFloat 59: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 59: [ RUN ] ReadTest.get_ereal_WarnsAboutString 59: 59: ERROR 1 [file unknown]: 59: Right hand side 'hello' for parameter 'test' in parameter file is not a 59: real value 59: 59: 59: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 59: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 59: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 59: [----------] 10 tests from ReadTest (0 ms total) 59: 59: [----------] 3 tests from TimeControlTest 59: [ RUN ] TimeControlTest.UnSetHasNoValue 59: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 59: [ RUN ] TimeControlTest.CanSetValue 59: [ OK ] TimeControlTest.CanSetValue (0 ms) 59: [ RUN ] TimeControlTest.CanUnsetValueAgain 59: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 59: [----------] 3 tests from TimeControlTest (0 ms total) 59: 59: [----------] 1 test from FileIOXdrSerializerTest 59: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 59: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 59: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 59: 59: [----------] 1 test from TngTest 59: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 59: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 59: [----------] 1 test from TngTest (0 ms total) 59: 59: [----------] 4 tests from XvgioTest 59: [ RUN ] XvgioTest.readXvgIntWorks 59: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgRealWorks 59: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 59: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 59: [ RUN ] XvgioTest.readXvgDeprecatedWorks 59: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 59: [----------] 4 tests from XvgioTest (0 ms total) 59: 59: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (13 ms) 59: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 59: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 59: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (14 ms total) 59: 59: [----------] 360 tests from FileTypeMatch/FileTypeTest 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 59: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 59: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 59: [----------] 360 tests from FileTypeMatch/FileTypeTest (0 ms total) 59: 59: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 59: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 59: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 59: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (0 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 413 tests from 15 test suites ran. (18 ms total) 59: [ PASSED ] 413 tests. 59/87 Test #59: FileIOTests ............................... Passed 0.11 sec test 60 Start 60: SelectionUnitTests 60: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/tests 60: Test timeout computed to be: 30 60: [==========] Running 201 tests from 11 test suites. 60: [----------] Global test environment set-up. 60: [----------] 1 test from IndexGroupTest 60: [ RUN ] IndexGroupTest.RemovesDuplicates 60: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 60: [----------] 1 test from IndexGroupTest (0 ms total) 60: 60: [----------] 15 tests from IndexBlockTest 60: [ RUN ] IndexBlockTest.CreatesUnknownBlock 60: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 60: [ RUN ] IndexBlockTest.CreatesAtomBlock 60: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 60: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 60: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 60: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 60: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 60: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 60: [ RUN ] IndexBlockTest.CreatesSingleBlock 60: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 60: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 60: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 60: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 60: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 60: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 60: [----------] 15 tests from IndexBlockTest (0 ms total) 60: 60: [----------] 11 tests from IndexMapTest 60: [ RUN ] IndexMapTest.InitializesAtomBlock 60: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 60: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 60: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 60: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 60: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 60: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 60: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 60: [ RUN ] IndexMapTest.InitializesMoleculeBlock 60: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 60: [ RUN ] IndexMapTest.MapsSingleBlock 60: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 60: [ RUN ] IndexMapTest.MapsResidueBlocks 60: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 60: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 60: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 60: [ RUN ] IndexMapTest.HandlesMultipleRequests 60: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 60: [----------] 11 tests from IndexMapTest (1 ms total) 60: 60: [----------] 3 tests from IndexGroupsAndNamesTest 60: [ RUN ] IndexGroupsAndNamesTest.containsNames 60: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 60: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 60: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms) 60: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 60: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 60: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total) 60: 60: [----------] 15 tests from NeighborhoodSearchTest 60: [ RUN ] NeighborhoodSearchTest.SimpleSearch 60: [ OK ] NeighborhoodSearchTest.SimpleSearch (37 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 60: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (32 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchBox 60: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 60: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (12 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 60: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (14 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 60: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 60: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (1 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 60: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (8 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 60: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (77 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 60: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 60: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 60: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 60: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 60: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 60: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 60: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 60: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 60: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 60: [----------] 15 tests from NeighborhoodSearchTest (189 ms total) 60: 60: [----------] 13 tests from PositionCalculationTest 60: [ RUN ] PositionCalculationTest.ComputesAtomPositions 60: [ OK ] PositionCalculationTest.ComputesAtomPositions (16 ms) 60: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 60: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 60: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 60: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 60: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 60: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 60: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 60: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 60: [ RUN ] PositionCalculationTest.ComputesPositionMask 60: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 60: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 60: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 60: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 60: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 60: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 60: [----------] 13 tests from PositionCalculationTest (17 ms total) 60: 60: [----------] 33 tests from SelectionCollectionTest 60: [ RUN ] SelectionCollectionTest.HandlesNoSelections 60: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 60: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 60: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 60: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 60: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 60: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 60: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 60: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 60: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (8 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 60: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 60: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 60: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 60: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 60: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 60: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 60: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 60: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 60: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 60: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 60: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 60: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 60: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 60: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 60: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 60: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 60: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (12 ms) 60: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 60: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 60: [----------] 33 tests from SelectionCollectionTest (26 ms total) 60: 60: [----------] 14 tests from SelectionCollectionInteractiveTest 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 60: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 60: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 60: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 60: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 60: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 60: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 60: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 60: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 60: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 60: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (0 ms) 60: [----------] 14 tests from SelectionCollectionInteractiveTest (2 ms total) 60: 60: [----------] 70 tests from SelectionCollectionDataTest 60: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 60: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 60: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResnr 60: [ OK ] SelectionCollectionDataTest.HandlesResnr (12 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 60: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 60: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 60: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 60: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 60: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesChain 60: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMass 60: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesCharge 60: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 60: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 60: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 60: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBeta 60: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesResname 60: [ OK ] SelectionCollectionDataTest.HandlesResname (12 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 60: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 60: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 60: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (9 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 60: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (13 ms) 60: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 60: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 60: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 60: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 60: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 60: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 60: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 60: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 60: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (8 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 60: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 60: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 60: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 60: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 60: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 60: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 60: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 60: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 60: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (12 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 60: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 60: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 60: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 60: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 60: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 60: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 60: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 60: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 60: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 60: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (8 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 60: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 60: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 60: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 60: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 60: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 60: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (12 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (0 ms) 60: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 60: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (0 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (0 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (0 ms) 60: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 60: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (9 ms) 60: [----------] 70 tests from SelectionCollectionDataTest (125 ms total) 60: 60: [----------] 17 tests from SelectionOptionTest 60: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 60: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 60: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 60: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 60: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksEmptySelections 60: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 60: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 60: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (10 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooManySelections 60: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 60: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 60: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesAdjuster 60: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 60: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 60: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 60: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 60: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 60: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 60: [----------] 17 tests from SelectionOptionTest (12 ms total) 60: 60: [----------] 9 tests from SelectionFileOptionTest 60: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 60: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 60: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 60: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 60: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 60: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 60: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 60: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 60: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 60: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 60: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 60: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 60: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 201 tests from 11 test suites ran. (378 ms total) 60: [ PASSED ] 201 tests. 60/87 Test #60: SelectionUnitTests ........................ Passed 0.45 sec test 61 Start 61: MdrunOutputTests 61: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 61: Test timeout computed to be: 600 61: [==========] Running 12 tests from 5 test suites. 61: [----------] Global test environment set-up. 61: [----------] 1 test from MdrunTest 61: [ RUN ] MdrunTest.WritesHelp 61: [ OK ] MdrunTest.WritesHelp (49 ms) 61: [----------] 1 test from MdrunTest (49 ms total) 61: 61: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to -1115684881 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.056 0.028 199.5 61: (ns/day) (hour/ns) 61: Performance: 6.199 3.872 61: Reading frame 0 time 0.000 61: # Atoms 6 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (85 ms) 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to 728721659 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 21 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.082 0.041 199.7 61: (ns/day) (hour/ns) 61: Performance: 4.192 5.726 61: Reading frame 0 time 0.000 61: # Atoms 6 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (76 ms) 61: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 61: Generating 1-4 interactions: fudge = 0.5 61: Number of degrees of freedom in T-Coupling group rest is 9.00 61: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 61: NVE simulation: will use the initial temperature of 2573.591 K for 61: determining the Verlet buffer size 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There were 2 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc2' 61: 1 steps, 0.0 ps. 61: Setting the LD random seed to 1072159966 61: 61: Generated 3 of the 3 non-bonded parameter combinations 61: 61: Generated 3 of the 3 1-4 parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 23 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.086 0.043 199.6 61: (ns/day) (hour/ns) 61: Performance: 3.994 6.009 61: Reading frame 0 time 0.000 61: # Atoms 3 61: Reading frame 1 time 0.001 Last frame 1 time 0.001 61: 61: 61: Item #frames Timestep (ps) 61: Step 2 0.001 61: Time 2 0.001 61: Lambda 0 61: Coords 2 0.001 61: Velocities 0 61: Forces 0 61: Box 2 0.001 61: Checking file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 61: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (80 ms) 61: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (242 ms total) 61: 61: [----------] 2 tests from Argon12/OutputFiles 61: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Number of degrees of freedom in T-Coupling group System is 33.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 61: NVE simulation: will use the initial temperature of 68.810 K for 61: determining the Verlet buffer size 61: 61: 61: There were 3 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Argon' 61: 16 steps, 0.0 ps. 61: Generated 1 of the 1 non-bonded parameter combinations 61: 61: Excluding 1 bonded neighbours molecule type 'Argon' 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.382 0.191 199.9 61: (ns/day) (hour/ns) 61: Performance: 7.679 3.125 61: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (230 ms) 61: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 61: that with the Verlet scheme, nstlist has no effect on the accuracy of 61: your simulation. 61: 61: 61: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: Setting nstcalcenergy (100) equal to nstenergy (4) 61: 61: Number of degrees of freedom in T-Coupling group System is 33.00 61: 61: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 61: NVE simulation: will use the initial temperature of 68.810 K for 61: determining the Verlet buffer size 61: 61: 61: There were 3 NOTEs 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Can not increase nstlist because an NVE ensemble is used 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'Argon' 61: 16 steps, 0.0 ps. 61: Generated 1 of the 1 non-bonded parameter combinations 61: 61: Excluding 1 bonded neighbours molecule type 'Argon' 61: 61: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 61: 61: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.331 0.166 200.0 61: (ns/day) (hour/ns) 61: Performance: 8.867 2.707 61: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (188 ms) 61: [----------] 2 tests from Argon12/OutputFiles (419 ms total) 61: 61: [----------] 3 tests from MdrunCanWrite/Trajectories 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -56115481 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.152 0.076 199.9 61: (ns/day) (hour/ns) 61: Performance: 7.929 3.027 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (113 ms) 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -1208091145 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.163 0.082 199.9 61: (ns/day) (hour/ns) 61: Performance: 7.400 3.243 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (111 ms) 61: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 6 steps, 0.0 ps. 61: Setting the LD random seed to -1621426773 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.144 0.072 199.8 61: (ns/day) (hour/ns) 61: Performance: 8.373 2.866 61: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (103 ms) 61: [----------] 3 tests from MdrunCanWrite/Trajectories (338 ms total) 61: 61: [----------] 3 tests from MdrunCanWrite/NptTrajectories 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to 1878521727 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: NOTE: 12 % of the run time was spent in pair search, 61: you might want to increase nstlist (this has no effect on accuracy) 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.119 0.059 199.8 61: (ns/day) (hour/ns) 61: Performance: 4.360 5.505 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (94 ms) 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 61: 61: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 61: The Berendsen barostat does not generate any strictly correct ensemble, 61: and should not be used for new production simulations (in our opinion). 61: We recommend using the C-rescale barostat instead. 61: 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: 61: There was 1 WARNING 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -1254589195 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.079 0.040 199.7 61: (ns/day) (hour/ns) 61: Performance: 6.512 3.685 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (85 ms) 61: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 61: Number of degrees of freedom in T-Coupling group System is 12.00 61: 61: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 61: You are using a plain Coulomb cut-off, which might produce artifacts. 61: You might want to consider using PME electrostatics. 61: 61: 61: 61: There was 1 NOTE 61: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 61: Changing nstlist from 10 to 40, rlist from 1.034 to 1.183 61: 61: Using 1 MPI thread 61: Using 2 OpenMP threads 61: 61: 61: NOTE: The number of threads is not equal to the number of (logical) cpus 61: and the -pin option is set to auto: will not pin threads to cpus. 61: This can lead to significant performance degradation. 61: Consider using -pin on (and -pinoffset in case you run multiple jobs). 61: starting mdrun 'spc-and-methanol' 61: 2 steps, 0.0 ps. 61: Setting the LD random seed to -335564801 61: 61: Generated 8 of the 10 non-bonded parameter combinations 61: 61: Excluding 2 bonded neighbours molecule type 'Methanol' 61: 61: Excluding 2 bonded neighbours molecule type 'SOL' 61: 61: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 61: 61: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 61: 61: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 61: 61: Note that mdrun will redetermine rlist based on the actual pair-list setup 61: 61: This run will generate roughly 0 Mb of data 61: 61: Writing final coordinates. 61: 61: Core t (s) Wall t (s) (%) 61: Time: 0.074 0.037 199.7 61: (ns/day) (hour/ns) 61: Performance: 6.984 3.437 61: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (65 ms) 61: [----------] 3 tests from MdrunCanWrite/NptTrajectories (245 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 12 tests from 5 test suites ran. (1388 ms total) 61: [ PASSED ] 12 tests. 61/87 Test #61: MdrunOutputTests .......................... Passed 1.44 sec test 62 Start 62: MdrunModulesTests 62: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 62: Test timeout computed to be: 600 62: [==========] Running 15 tests from 3 test suites. 62: [----------] Global test environment set-up. 62: [----------] 9 tests from DensityFittingTest 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -3.85652608067156e+03 62: Maximum force = 4.50998690851897e+03 on atom 3 62: Norm of force = 1.68168494163492e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -369133726 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (51 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -9.82077921283928e+03 62: Maximum force = 7.39548334240075e+03 on atom 2 62: Norm of force = 2.78250777177324e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -35691649 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (37 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (24 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Overriding nsteps with value passed on the command line: 4 steps 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 4 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 5 steps. 62: Potential Energy = -1.09549987768583e+04 62: Maximum force = 7.47247842297763e+03 on atom 2 62: Norm of force = 2.77579925913607e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -612433987 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (41 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (30 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -3.85652608067156e+03 62: Maximum force = 4.50998690851897e+03 on atom 3 62: Norm of force = 1.68168494163492e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -1107347633 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (28 ms) 62: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = -2.71386626041483e+04 62: Maximum force = 6.78276506555709e+03 on atom 2 62: Norm of force = 1.96088641457984e+03 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -285755503 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (31 ms) 62: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 62: 62: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:1108:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads. See https://github.com/google/googletest/blob/main/docs/advanced.md#death-tests-and-threads for more explanation and suggested solutions, especially if this is the last message you see before your test times out. 62: Setting the LD random seed to -537397561 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (35 ms) 62: [ RUN ] DensityFittingTest.CheckpointWorks 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 62: Setting nstcalcenergy (100) equal to nstenergy (2) 62: 62: Number of degrees of freedom in T-Coupling group rest is 33.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 62: NVE simulation: will use the initial temperature of 68.810 K for 62: determining the Verlet buffer size 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Argon' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to -8932875 62: 62: Generated 1 of the 1 non-bonded parameter combinations 62: 62: Excluding 1 bonded neighbours molecule type 'Argon' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: NOTE: 29 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.048 0.024 199.5 62: (ns/day) (hour/ns) 62: Performance: 10.704 2.242 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 62: Can not increase nstlist because an NVE ensemble is used 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting mdrun 'Argon' 62: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.037 0.018 199.4 62: (ns/day) (hour/ns) 62: Performance: 23.358 1.027 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (67 ms) 62: [----------] 9 tests from DensityFittingTest (350 ms total) 62: 62: [----------] 4 tests from MimicTest 62: [ RUN ] MimicTest.OneQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 44 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.008 0.004 198.4 62: (ns/day) (hour/ns) 62: Performance: 22.665 1.059 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -12649537 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.OneQuantumMol (10 ms) 62: [ RUN ] MimicTest.AllQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 43 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.008 0.004 198.4 62: (ns/day) (hour/ns) 62: Performance: 22.132 1.084 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -302781777 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.AllQuantumMol (11 ms) 62: [ RUN ] MimicTest.TwoQuantumMol 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 21.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: NVE simulation with an initial temperature of zero: will use a Verlet 62: buffer of 10%. Check your energy drift! 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 62: 62: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 43 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.008 0.004 198.5 62: (ns/day) (hour/ns) 62: Performance: 22.121 1.085 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -201327105 62: 62: Generated 10 of the 10 non-bonded parameter combinations 62: 62: Generated 10 of the 10 1-4 parameter combinations 62: 62: Excluding 2 bonded neighbours molecule type 'SOL' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.TwoQuantumMol (13 ms) 62: [ RUN ] MimicTest.BondCuts 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: For a correct single-point energy evaluation with nsteps = 0, use 62: continuation = yes to avoid constraining the input coordinates. 62: 62: Generating 1-4 interactions: fudge = 0.5 62: Number of degrees of freedom in T-Coupling group rest is 66.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: NVE simulation: will use the initial temperature of 300.368 K for 62: determining the Verlet buffer size 62: 62: 62: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 3 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Can not increase nstlist because an NVE ensemble is used 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 62: 62: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 62: Reading frame 0 time 0.000 Last frame 0 time 0.000 62: 62: NOTE: 36 % of the run time was spent in pair search, 62: you might want to increase nstlist (this has no effect on accuracy) 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.009 0.005 198.9 62: (ns/day) (hour/ns) 62: Performance: 18.165 1.321 62: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 62: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2080371679 62: 62: Generated 2211 of the 2211 non-bonded parameter combinations 62: 62: Generated 2211 of the 2211 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] MimicTest.BondCuts (20 ms) 62: [----------] 4 tests from MimicTest (57 ms total) 62: 62: [----------] 2 tests from WithIntegrator/ImdTest 62: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 62: Generating 1-4 interactions: fudge = 1 62: 62: NOTE 1 [file glycine_vacuo.top, line 12]: 62: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 62: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 62: the time step of 2.0e-03 ps. 62: Maybe you forgot to change the constraints mdp option. 62: 62: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 62: Number of degrees of freedom in T-Coupling group System is 27.00 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Changing nstlist from 10 to 25, rlist from 1.077 to 1.248 62: 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: IMD: Enabled. This simulation will accept incoming IMD connections. 62: IMD: Pulling from IMD remote is enabled (-imdpull). 62: IMD: Setting port for connection requests to 0. 62: IMD: Setting up incoming socket. 62: IMD: Listening for IMD connection on port 59911. 62: IMD: -imdwait not set, starting simulation. 62: starting mdrun 'Glycine' 62: 2 steps, 0.0 ps. 62: Setting the LD random seed to -1619265793 62: 62: Generated 20503 of the 20503 non-bonded parameter combinations 62: 62: Generated 17396 of the 20503 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Glycine' 62: 62: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 62: 62: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 62: 62: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 62: 62: Note that mdrun will redetermine rlist based on the actual pair-list setup 62: 62: This run will generate roughly 0 Mb of data 62: 62: Writing final coordinates. 62: 62: Core t (s) Wall t (s) (%) 62: Time: 0.034 0.017 199.2 62: (ns/day) (hour/ns) 62: Performance: 29.989 0.800 62: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (95 ms) 62: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 62: 62: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 62: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 62: apply to steep. 62: 62: Generating 1-4 interactions: fudge = 1 62: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 62: Number of degrees of freedom in T-Coupling group System is 27.00 62: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 62: 62: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 62: You are using a plain Coulomb cut-off, which might produce artifacts. 62: You might want to consider using PME electrostatics. 62: 62: 62: 62: There were 2 NOTEs 62: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 62: Using 1 MPI thread 62: Using 2 OpenMP threads 62: 62: 62: NOTE: The number of threads is not equal to the number of (logical) cpus 62: and the -pin option is set to auto: will not pin threads to cpus. 62: This can lead to significant performance degradation. 62: Consider using -pin on (and -pinoffset in case you run multiple jobs). 62: 62: IMD: Enabled. This simulation will accept incoming IMD connections. 62: IMD: Pulling from IMD remote is enabled (-imdpull). 62: IMD: Setting port for connection requests to 0. 62: IMD: Setting up incoming socket. 62: IMD: Listening for IMD connection on port 59395. 62: IMD: -imdwait not set, starting simulation. 62: 62: Steepest Descents: 62: Tolerance (Fmax) = 1.00000e+01 62: Number of steps = 2 62: 62: Energy minimization reached the maximum number of steps before the forces 62: reached the requested precision Fmax < 10. 62: 62: writing lowest energy coordinates. 62: 62: Steepest Descents did not converge to Fmax < 10 in 3 steps. 62: Potential Energy = 1.19770464690297e+03 62: Maximum force = 1.77948604657896e+04 on atom 9 62: Norm of force = 7.87328617833980e+03 62: Setting the LD random seed to -1356603982 62: 62: Generated 20503 of the 20503 non-bonded parameter combinations 62: 62: Generated 17396 of the 20503 1-4 parameter combinations 62: 62: Excluding 3 bonded neighbours molecule type 'Glycine' 62: 62: This run will generate roughly 0 Mb of data 62: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (87 ms) 62: [----------] 2 tests from WithIntegrator/ImdTest (183 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 15 tests from 3 test suites ran. (641 ms total) 62: [ PASSED ] 15 tests. 62/87 Test #62: MdrunModulesTests ......................... Passed 0.69 sec test 63 Start 63: MdrunIOTests 63: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunIOTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 76 tests from 13 test suites. 63: [----------] Global test environment set-up. 63: [----------] 9 tests from GromppTest 63: [ RUN ] GromppTest.EmptyMdpFileWorks 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -1082201281 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.EmptyMdpFileWorks (3 ms) 63: [ RUN ] GromppTest.SimulatedAnnealingWorks 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Simulated annealing for group rest: Periodic, 4 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 2.0 320.0 63: 4.0 320.0 63: 6.0 298.0 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -537526337 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.SimulatedAnnealingWorks (6 ms) 63: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Simulated annealing for group Methanol: Single, 3 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 3.0 280.0 63: 6.0- 270.0 63: Simulated annealing for group SOL: Periodic, 4 timepoints 63: Time (ps) Temperature (K) 63: 0.0 298.0 63: 2.0 320.0 63: 4.0 320.0 63: 6.0 298.0 63: Number of degrees of freedom in T-Coupling group Methanol is 7.20 63: Number of degrees of freedom in T-Coupling group SOL is 4.80 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -1660970114 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (2 ms) 63: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 63: Setting the LD random seed to 1204723647 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (33 ms) 63: [ RUN ] GromppTest.HandlesMaxwarn 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: 63: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: The Berendsen thermostat does not generate the correct kinetic energy 63: distribution, and should not be used for new production simulations (in 63: our opinion). We would recommend the V-rescale thermostat. 63: 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: 63: There was 1 WARNING 63: Setting the LD random seed to -681577121 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 63: [ RUN ] GromppTest.MaxwarnShouldBePositive 63: [ OK ] GromppTest.MaxwarnShouldBePositive (0 ms) 63: [ RUN ] GromppTest.ValidTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Pull group 1 'SOL' has 3 atoms 63: Pull group 2 'Methanol' has 3 atoms 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 63: There were 3 NOTEs 63: Setting the LD random seed to -2425245 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: [ OK ] GromppTest.ValidTransformationCoord (11 ms) 63: [ RUN ] GromppTest.InvalidTransformationCoord 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: For a correct single-point energy evaluation with nsteps = 0, use 63: continuation = yes to avoid constraining the input coordinates. 63: 63: Pull group 1 'SOL' has 3 atoms 63: Pull group 2 'Methanol' has 3 atoms 63: Number of degrees of freedom in T-Coupling group rest is 12.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: NVE simulation: will use the initial temperature of 1046.791 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 5 63: 2 3 2 0.613 nm 0.000 nm 63: 1 3 5 63: 2 3 2 Setting the LD random seed to -542115526 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: [ OK ] GromppTest.InvalidTransformationCoord (15 ms) 63: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 63: Setting the LD random seed to -813699924 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (18 ms) 63: [----------] 9 tests from GromppTest (93 ms total) 63: 63: [----------] 6 tests from MdrunTerminationTest 63: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to 1005567931 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 26 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.057 0.028 199.5 63: (ns/day) (hour/ns) 63: Performance: 9.137 2.627 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.026 199.5 63: (ns/day) (hour/ns) 63: Performance: 10.077 2.382 63: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (151 ms) 63: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 1, rlist from 1.035 to 1 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 100 steps, 0.1 ps. 63: 63: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 63: Setting the LD random seed to 528334677 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: NOTE: 56 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.047 0.024 199.5 63: (ns/day) (hour/ns) 63: Performance: 7.284 3.295 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 102 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 100 63: Runtime for the run 0.1 ps 63: Run end step 100 63: Run end time 0.1 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 102 63: Runtime for the run 0.102 ps 63: Run end step 102 63: Run end time 0.102 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.561 0.781 200.0 63: (ns/day) (hour/ns) 63: Performance: 11.288 2.126 63: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (838 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to 1585225407 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.071 0.036 199.5 63: (ns/day) (hour/ns) 63: Performance: 7.273 3.300 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: NOTE: 31 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.7 63: (ns/day) (hour/ns) 63: Performance: 8.081 2.970 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 6 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 6 63: Runtime for the run 0.006 ps 63: Run end step 6 63: Run end time 0.006 ps 63: 63: 63: Writing final coordinates. 63: 63: NOTE: 21 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.079 0.040 199.7 63: (ns/day) (hour/ns) 63: Performance: 6.557 3.660 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 8 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 6 63: Runtime for the run 0.006 ps 63: Run end step 6 63: Run end time 0.006 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 8 63: Runtime for the run 0.008 ps 63: Run end step 8 63: Run end time 0.008 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.067 0.033 199.8 63: (ns/day) (hour/ns) 63: Performance: 7.765 3.091 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.024 0.012 199.2 63: (ns/day) (hour/ns) 63: Performance: 7.033 3.412 63: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (223 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -171984153 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.6 63: (ns/day) (hour/ns) 63: Performance: 8.067 2.975 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps. 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.105 0.052 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.236 2.914 63: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (137 ms) 63: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -137691331 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 28 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.068 0.034 199.7 63: (ns/day) (hour/ns) 63: Performance: 7.639 3.142 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (58 ms) 63: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -18173577 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.074 0.037 199.6 63: (ns/day) (hour/ns) 63: Performance: 6.977 3.440 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Setting nsteps to 4 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 10 to 40, rlist from 1.035 to 1.179 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 63: Input file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 2 63: Runtime for the run 0.002 ps 63: Run end step 2 63: Run end time 0.002 ps 63: 63: 63: Output file: 63: Run start step 0 63: Run start time 0 ps 63: Step to be made during run 4 63: Runtime for the run 0.004 ps 63: Run end step 4 63: Run end time 0.004 ps 63: 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.054 0.027 199.7 63: (ns/day) (hour/ns) 63: Performance: 9.531 2.518 63: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (115 ms) 63: [----------] 6 tests from MdrunTerminationTest (1525 ms total) 63: 63: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 63: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.331 0.166 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.871 2.705 63: trr version: GMX_trn_file (double precision) 63: 63: 63: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (199 ms) 63: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.411 0.205 200.0 63: (ns/day) (hour/ns) 63: Performance: 7.152 3.356 63: 63: 63: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (233 ms) 63: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (433 ms total) 63: 63: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.177 0.088 199.9 63: (ns/day) (hour/ns) 63: Performance: 16.603 1.446 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 18 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.098 0.049 199.8 63: (ns/day) (hour/ns) 63: Performance: 15.851 1.514 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.097 0.049 199.7 63: (ns/day) (hour/ns) 63: Performance: 16.005 1.500 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (241 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.175 0.088 199.9 63: (ns/day) (hour/ns) 63: Performance: 16.766 1.431 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.101 0.050 199.8 63: (ns/day) (hour/ns) 63: Performance: 15.437 1.555 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.103 0.051 199.8 63: (ns/day) (hour/ns) 63: Performance: 15.139 1.585 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (225 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.201 0.100 199.9 63: (ns/day) (hour/ns) 63: Performance: 14.625 1.641 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.113 0.056 199.9 63: (ns/day) (hour/ns) 63: Performance: 13.803 1.739 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.107 0.054 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.478 1.658 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (244 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.198 0.099 199.9 63: (ns/day) (hour/ns) 63: Performance: 14.802 1.621 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.119 0.060 199.9 63: (ns/day) (hour/ns) 63: Performance: 13.061 1.838 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.137 0.069 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.313 2.121 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (262 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.262 0.131 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.192 2.144 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.160 0.080 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.733 2.466 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.138 0.069 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.280 2.128 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (343 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.263 0.132 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.165 2.150 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.134 0.067 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.628 2.064 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.709 to 0.735 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.150 0.075 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.381 2.312 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (318 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.282 0.141 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.399 2.308 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.161 0.080 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.666 2.483 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.155 0.078 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.021 2.395 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (339 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.346 0.173 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.487 2.828 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.156 0.078 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.951 2.412 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.153 0.076 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.170 2.360 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (376 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.315 0.158 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.315 2.577 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.163 0.082 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.511 2.523 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.167 0.084 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.280 2.586 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (383 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.302 0.151 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.713 2.471 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.171 0.085 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.099 2.638 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.159 0.080 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.753 2.461 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (384 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.387 0.194 200.0 63: (ns/day) (hour/ns) 63: Performance: 7.587 3.163 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 17 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.202 0.101 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.702 3.116 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.197 0.099 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.884 3.044 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (457 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.282 0.141 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.430 2.301 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.148 0.074 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.511 2.283 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.146 0.073 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.609 2.262 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (339 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.221 0.111 199.9 63: (ns/day) (hour/ns) 63: Performance: 13.257 1.810 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.116 0.058 199.8 63: (ns/day) (hour/ns) 63: Performance: 13.372 1.795 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.115 0.058 199.8 63: (ns/day) (hour/ns) 63: Performance: 13.479 1.781 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (271 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.210 0.105 199.9 63: (ns/day) (hour/ns) 63: Performance: 14.013 1.713 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.109 0.055 199.8 63: (ns/day) (hour/ns) 63: Performance: 14.257 1.683 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.73 to 0.814 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.115 0.058 199.8 63: (ns/day) (hour/ns) 63: Performance: 13.509 1.777 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (269 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.271 0.136 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.826 2.217 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.139 0.070 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.158 2.151 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.147 0.074 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.555 2.274 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (331 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.253 0.126 199.9 63: (ns/day) (hour/ns) 63: Performance: 11.626 2.064 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.092 0.046 199.8 63: (ns/day) (hour/ns) 63: Performance: 16.859 1.424 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.753 to 0.895 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.084 0.042 199.7 63: (ns/day) (hour/ns) 63: Performance: 18.407 1.304 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (257 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.723 0.361 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.065 5.904 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.461 0.231 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.373 7.115 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.458 0.229 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.395 7.070 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (971 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.687 0.343 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.277 5.612 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.445 0.223 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.493 6.872 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.351 0.176 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.425 5.424 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (886 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.793 0.396 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.705 6.478 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.285 0.142 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.461 4.395 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.321 0.161 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.836 4.962 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (800 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: NVE simulation: will use the initial temperature of 456.887 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 6 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.556 0.278 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.282 4.544 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.295 0.148 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.264 4.559 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.457 0.229 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.403 7.053 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (742 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.668 0.334 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.396 5.460 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.364 0.182 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.266 5.625 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.439 0.220 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.539 6.782 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (895 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.886 0.443 200.0 63: (ns/day) (hour/ns) 63: Performance: 3.313 7.243 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 80, rlist from 0.743 to 0.847 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.475 0.238 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.271 7.338 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 80, rlist from 0.743 to 0.846 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.371 0.186 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.188 5.730 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (1303 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.386 0.693 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.119 11.327 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.786 0.393 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.979 12.127 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.587 0.293 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.650 9.057 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (1567 ms) 63: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: 63: NOTE 3 [file unknown]: 63: You are using constraints on all bonds, whereas the forcefield has been 63: parametrized only with constraints involving hydrogen atoms. We suggest 63: using constraints = h-bonds instead, this will also improve performance. 63: 63: Number of degrees of freedom in T-Coupling group System is 23.00 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: There are 9 non-linear virtual site constructions. Their contribution to 63: the energy error is approximated. In most cases this does not affect the 63: error significantly. 63: 63: 63: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 5 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 63: 63: turning all bonds into constraints... 63: 63: Cleaning up constraints and constant bonded interactions with virtual sites 63: 63: Removed 18 Angles with virtual sites, 21 left 63: 63: Removed 10 Proper Dih.s with virtual sites, 44 left 63: 63: Converted 15 Constraints with virtual sites to connections, 7 left 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.245 0.623 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.359 10.176 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.766 0.383 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.029 11.827 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 25, rlist from 0.725 to 0.797 63: 63: Update groups can not be used for this system because an incompatible virtual site type is used 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine dipeptide in vacuo' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.833 0.416 200.0 63: (ns/day) (hour/ns) 63: Performance: 1.867 12.854 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (1671 ms) 63: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (13886 ms total) 63: 63: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.363 0.182 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.079 2.971 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.222 0.111 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.988 3.434 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.261 0.130 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.962 4.026 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (538 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.373 0.187 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.872 3.049 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 18 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.195 0.098 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.955 3.017 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.200 0.100 199.8 63: (ns/day) (hour/ns) 63: Performance: 7.770 3.089 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (494 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.463 0.232 200.0 63: (ns/day) (hour/ns) 63: Performance: 6.339 3.786 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.259 0.129 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.008 3.995 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.275 0.138 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.652 4.246 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (599 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: NVE simulation: will use the initial temperature of 293.480 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 4 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.472 0.236 200.0 63: (ns/day) (hour/ns) 63: Performance: 6.219 3.859 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.286 0.143 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.444 4.408 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.311 0.156 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.997 4.803 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (638 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.475 0.238 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.182 3.882 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.279 0.140 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.569 4.310 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.257 0.129 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.046 3.970 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (668 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.449 0.225 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.542 3.669 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.214 0.107 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.251 3.310 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.729 to 0.809 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.189 0.095 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.213 2.922 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (845 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.462 0.231 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.353 3.778 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.451 0.226 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.445 6.968 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.487 0.244 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.192 7.519 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (859 ms) 63: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.614 0.307 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.780 5.021 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.344 0.172 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.520 5.310 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 20, rlist from 0.751 to 0.848 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.326 0.163 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.764 5.038 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (839 ms) 63: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (5485 ms total) 63: 63: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.297 0.149 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.889 2.427 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.226 0.113 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.884 3.486 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 19 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.234 0.117 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.653 3.607 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (473 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.358 0.179 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.214 2.922 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.200 0.100 199.8 63: (ns/day) (hour/ns) 63: Performance: 7.769 3.089 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.196 0.098 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.928 3.027 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (453 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.306 0.153 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.606 2.498 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.181 0.091 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.587 2.795 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.170 0.085 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.133 2.628 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (399 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.296 0.148 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.931 2.417 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.152 0.076 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.219 2.349 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.162 0.081 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.563 2.510 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (375 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.294 0.147 200.0 63: (ns/day) (hour/ns) 63: Performance: 9.995 2.401 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.159 0.079 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.791 2.451 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 19 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.150 0.075 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.390 2.310 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (347 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.267 0.134 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.983 2.185 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.149 0.075 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.432 2.301 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.145 0.073 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.712 2.241 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (331 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.234 0.117 199.9 63: (ns/day) (hour/ns) 63: Performance: 12.549 1.912 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.084 0.042 199.8 63: (ns/day) (hour/ns) 63: Performance: 18.607 1.290 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.083 0.042 199.7 63: (ns/day) (hour/ns) 63: Performance: 18.690 1.284 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (235 ms) 63: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.154 0.077 199.9 63: (ns/day) (hour/ns) 63: Performance: 19.034 1.261 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.085 0.042 199.8 63: (ns/day) (hour/ns) 63: Performance: 18.327 1.310 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Changing nstlist from 8 to 100, rlist from 0.702 to 0.74 63: 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.079 0.040 199.7 63: (ns/day) (hour/ns) 63: Performance: 19.596 1.225 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (181 ms) 63: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (2798 ms total) 63: 63: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 63: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.121 0.060 199.8 63: (ns/day) (hour/ns) 63: Performance: 24.333 0.986 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.6 63: (ns/day) (hour/ns) 63: Performance: 24.111 0.995 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 10 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.6 63: (ns/day) (hour/ns) 63: Performance: 24.140 0.994 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (146 ms) 63: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.134 0.067 199.9 63: (ns/day) (hour/ns) 63: Performance: 21.914 1.095 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.075 0.038 199.8 63: (ns/day) (hour/ns) 63: Performance: 20.639 1.163 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.143 0.072 199.8 63: (ns/day) (hour/ns) 63: Performance: 10.829 2.216 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (196 ms) 63: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (343 ms total) 63: 63: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.355 0.178 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.270 2.902 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 13 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.182 0.091 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.519 2.817 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.172 0.086 199.8 63: (ns/day) (hour/ns) 63: Performance: 9.029 2.658 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (445 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.422 0.211 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.965 3.446 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.230 0.115 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.746 3.558 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.196 0.098 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.928 3.027 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (517 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.345 0.173 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.514 2.819 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 19 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.191 0.096 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.126 2.954 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.200 0.100 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.769 3.089 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (441 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 63: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 63: 1 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.353 0.176 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.327 2.882 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.118 0.059 199.8 63: (ns/day) (hour/ns) 63: Performance: 13.162 1.823 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.120 0.060 199.8 63: (ns/day) (hour/ns) 63: Performance: 12.931 1.856 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (347 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.215 0.107 199.9 63: (ns/day) (hour/ns) 63: Performance: 13.689 1.753 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 11 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.081 0.040 199.8 63: (ns/day) (hour/ns) 63: Performance: 19.290 1.244 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.077 0.039 199.6 63: (ns/day) (hour/ns) 63: Performance: 20.107 1.194 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (212 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.140 0.070 199.9 63: (ns/day) (hour/ns) 63: Performance: 20.901 1.148 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.077 0.039 199.8 63: (ns/day) (hour/ns) 63: Performance: 20.196 1.188 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.074 0.037 199.6 63: (ns/day) (hour/ns) 63: Performance: 20.964 1.145 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (165 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 63: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 63: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.274 0.137 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.700 2.243 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.202 0.101 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.691 3.121 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 17 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.191 0.096 199.8 63: (ns/day) (hour/ns) 63: Performance: 8.135 2.950 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (365 ms) 63: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (2496 ms total) 63: 63: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 63: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.657 0.328 200.0 63: (ns/day) (hour/ns) 63: Performance: 4.474 5.365 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.408 0.204 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.808 6.302 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.502 0.251 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.096 7.751 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (844 ms) 63: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (844 ms total) 63: 63: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 63: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.376 0.188 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.808 3.074 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: NOTE: 12 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.248 0.124 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.268 3.829 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: NOTE: 14 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.139 0.070 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.153 2.152 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (444 ms) 63: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'FirstWaterMolecule' has 3 atoms 63: Pull group 2 'SecondWaterMolecule' has 3 atoms 63: Number of degrees of freedom in T-Coupling group System is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 3 2 63: 2 3 5 1.112 nm 1.000 nm 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps. 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.489 0.244 200.0 63: (ns/day) (hour/ns) 63: Performance: 6.010 3.993 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.322 0.161 199.9 63: (ns/day) (hour/ns) 63: Performance: 4.821 4.978 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.247 0.123 199.9 63: (ns/day) (hour/ns) 63: Performance: 6.303 3.808 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (596 ms) 63: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (1041 ms total) 63: 63: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 63: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: Setting the AWH bias MC random seed to -528482601 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Setting the AWH bias MC random seed to -100663681 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.373 0.187 199.9 63: (ns/day) (hour/ns) 63: Performance: 7.868 3.050 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.253 0.127 199.8 63: (ns/day) (hour/ns) 63: Performance: 6.146 3.905 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.221 0.111 199.8 63: (ns/day) (hour/ns) 63: Performance: 7.030 3.414 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (571 ms) 63: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 63: Setting the AWH bias MC random seed to 2108620214 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Setting the AWH bias MC random seed to -537526865 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Pull group 1 'C_&_r_1' has 1 atoms 63: Pull group 2 'N_&_r_2' has 1 atoms 63: Pull group 3 'CA' has 1 atoms 63: Pull group 4 'C_&_r_2' has 1 atoms 63: Pull group 5 'N_&_r_3' has 1 atoms 63: Number of degrees of freedom in T-Coupling group System is 51.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: Pull group natoms pbc atom distance at start reference at t=0 63: 1 1 0 63: 2 1 0 179.098 deg 0.000 deg 63: 2 1 0 63: 3 1 0 158.667 deg 0.000 deg 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps. 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2145 of the 2145 non-bonded parameter combinations 63: 63: Generated 2145 of the 2145 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.522 0.261 199.9 63: (ns/day) (hour/ns) 63: Performance: 5.625 4.267 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.303 0.151 199.8 63: (ns/day) (hour/ns) 63: Performance: 5.135 4.674 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Alanine-dipeptide' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.456 0.228 199.9 63: (ns/day) (hour/ns) 63: Performance: 3.410 7.038 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (835 ms) 63: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (1407 ms total) 63: 63: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 63: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group System is 79.00 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps. 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: Generated 2485 of the 2485 non-bonded parameter combinations 63: 63: Generated 2485 of the 2485 1-4 parameter combinations 63: 63: Excluding 3 bonded neighbours molecule type 'nonanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 1.144 0.572 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.567 9.349 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 8 steps, 0.0 ps. 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.682 0.341 200.0 63: (ns/day) (hour/ns) 63: Performance: 2.280 10.524 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun '30 system in water' 63: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.726 0.363 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.143 11.201 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1560 ms) 63: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (1560 ms total) 63: 63: [----------] 3 tests from Checking/InitialConstraintsTest 63: [ RUN ] Checking/InitialConstraintsTest.Works/0 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to 2144795753 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 18 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.132 0.066 199.8 63: (ns/day) (hour/ns) 63: Performance: 2.619 9.164 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (149 ms) 63: [ RUN ] Checking/InitialConstraintsTest.Works/1 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -941181510 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.142 0.071 199.9 63: (ns/day) (hour/ns) 63: Performance: 2.440 9.837 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (109 ms) 63: [ RUN ] Checking/InitialConstraintsTest.Works/2 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: Integrator method md-vv-avek is implemented primarily for validation 63: purposes; for molecular dynamics, you should probably be using md or 63: md-vv 63: 63: Number of degrees of freedom in T-Coupling group rest is 11.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 1141.954 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI thread 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -1073743909 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: turning H bonds into constraints... 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: turning H bonds into constraints... 63: 63: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 25 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.064 0.032 199.5 63: (ns/day) (hour/ns) 63: Performance: 5.407 4.439 63: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 63: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (80 ms) 63: [----------] 3 tests from Checking/InitialConstraintsTest (339 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 76 tests from 13 test suites ran. (32629 ms total) 63: [ PASSED ] 76 tests. 63/87 Test #63: MdrunIOTests .............................. Passed 32.65 sec test 64 Start 64: MdrunTestsOneRank 64: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunTestsOneRank.xml" 64: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 28 tests from 7 test suites. 64: [----------] Global test environment set-up. 64: [----------] 1 test from CompelTest 64: [ RUN ] CompelTest.SwapCanRun 64: Generating 1-4 interactions: fudge = 0.5 64: Split0 group 'Ch0' contains 83 atoms. 64: Split1 group 'Ch1' contains 83 atoms. 64: Solvent group 'SOL' contains 11931 atoms. 64: Swap group 'NA+' contains 19 atoms. 64: Swap group 'CL-' contains 19 atoms. 64: Number of degrees of freedom in T-Coupling group System is 27869.00 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 64: Removing center of mass motion in the presence of position restraints 64: might cause artifacts. When you are using position restraints to 64: equilibrate a macro-molecule, the artifacts are usually negligible. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Update groups can not be used for this system because there are three or more consecutively coupled constraints 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: SWAP: Determining initial numbers of ions per compartment. 64: SWAP: Setting pointers for checkpoint writing 64: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 64: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 64: starting mdrun 'Channel_coco in octane membrane' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -1115686941 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein' 64: 64: turning all bonds into constraints... 64: 64: Excluding 3 bonded neighbours molecule type 'OCT' 64: 64: turning all bonds into constraints... 64: 64: Excluding 1 bonded neighbours molecule type 'NA' 64: 64: turning all bonds into constraints... 64: 64: Excluding 1 bonded neighbours molecule type 'CL' 64: 64: turning all bonds into constraints... 64: 64: Excluding 3 bonded neighbours molecule type 'Protein' 64: 64: Excluding 3 bonded neighbours molecule type 'OCT' 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning all bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 1 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 27 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 1.689 0.845 200.0 64: (ns/day) (hour/ns) 64: Performance: 1.535 15.640 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 64: 64: Update groups can not be used for this system because there are three or more consecutively coupled constraints 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: SWAP: Setting pointers for checkpoint writing 64: SWAP: Copying channel fluxes from checkpoint file data 64: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 64: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 64: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 64: starting mdrun 'Channel_coco in octane membrane' 64: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 64: 64: Writing final coordinates. 64: 64: NOTE: 14 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.926 0.463 200.0 64: (ns/day) (hour/ns) 64: Performance: 2.798 8.577 64: [ OK ] CompelTest.SwapCanRun (3377 ms) 64: [----------] 1 test from CompelTest (3377 ms total) 64: 64: [----------] 6 tests from BondedInteractionsTest 64: [ RUN ] BondedInteractionsTest.NormalBondWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 2 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 29 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.011 0.006 199.0 64: (ns/day) (hour/ns) 64: Performance: 15.090 1.590 64: Setting the LD random seed to -471864353 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalBondWorks (16 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 2 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 36 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.009 0.005 199.0 64: (ns/day) (hour/ns) 64: Performance: 18.689 1.284 64: Setting the LD random seed to -536912075 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedBondWorks (14 ms) 64: [ RUN ] BondedInteractionsTest.NormalAngleWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 28 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.012 0.006 199.1 64: (ns/day) (hour/ns) 64: Performance: 14.003 1.714 64: Setting the LD random seed to -976227843 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalAngleWorks (15 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 21 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.017 0.008 199.4 64: (ns/day) (hour/ns) 64: Performance: 10.201 2.353 64: Setting the LD random seed to 1606774175 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (18 ms) 64: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 72 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.022 0.011 199.5 64: (ns/day) (hour/ns) 64: Performance: 7.787 3.082 64: Setting the LD random seed to -336648417 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.NormalDihedralWorks (26 ms) 64: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: 64: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 64: In moleculetype 'butane' 4 atoms are not bound by a potential or 64: constraint to any other atom in the same moleculetype. Although 64: technically this might not cause issues in a simulation, this often means 64: that the user forgot to add a bond/potential/constraint or put multiple 64: molecules in the same moleculetype definition by mistake. Run with -v to 64: get information for each atom. 64: 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 64: 64: Reading frames from gro file 'A single butane', 4 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 67 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.018 0.009 199.5 64: (ns/day) (hour/ns) 64: Performance: 9.784 2.453 64: Setting the LD random seed to -53566081 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'butane' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (20 ms) 64: [----------] 6 tests from BondedInteractionsTest (111 ms total) 64: 64: [----------] 2 tests from BoxDeformationTest 64: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (10) 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 0 steps, 0.0 ps. 64: 64: NOTE: 61 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.026 0.013 199.3 64: (ns/day) (hour/ns) 64: Performance: 13.465 1.782 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -142944385 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Setting gen_seed to 2125410236 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (30 ms) 64: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (10) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 1293.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 20 steps, 0.0 ps. 64: Setting the LD random seed to 1191084013 64: 64: Generated 330891 of the 330891 non-bonded parameter combinations 64: 64: Generated 330891 of the 330891 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 64: 64: Estimate for the relative computational load of the PME mesh part: 0.18 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 1.257 0.628 200.0 64: (ns/day) (hour/ns) 64: Performance: 5.775 4.156 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (2132 ms) 64: [----------] 2 tests from BoxDeformationTest (2163 ms total) 64: 64: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -8405511 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.223 0.111 199.9 64: (ns/day) (hour/ns) 64: Performance: 3.879 6.187 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -1086620449 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 11 % of the run time was spent in domain decomposition, 64: 1 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.182 0.091 199.9 64: (ns/day) (hour/ns) 64: Performance: 4.731 5.073 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 64: 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (348 ms) 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -620824723 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.212 0.106 199.9 64: (ns/day) (hour/ns) 64: Performance: 4.076 5.888 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 2 [file ala.top, line 256]: 64: For energy conservation with LINCS, lincs_iter should be 2 or larger. 64: 64: 64: Number of degrees of freedom in T-Coupling group rest is 54.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 64: The optimal PME mesh load for parallel simulations is below 0.5 64: and for highly parallel simulations between 0.25 and 0.33, 64: for higher performance, increase the cut-off and the PME grid spacing. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'UNNAMED in water' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to 2079320311 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: turning H bonds into constraints... 64: 64: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 64: Calculating fourier grid dimensions for X Y Z 64: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 64: 64: Estimate for the relative computational load of the PME mesh part: 0.94 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.194 0.097 199.8 64: (ns/day) (hour/ns) 64: Performance: 4.456 5.386 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (327 ms) 64: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (676 ms total) 64: 64: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 64: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Pull group 1 'FirstWaterMolecule' has 3 atoms 64: Pull group 2 'SecondWaterMolecule' has 3 atoms 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Pull group natoms pbc atom distance at start reference at t=0 64: 1 3 2 64: 2 3 5 1.112 nm 1.000 nm 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -268550209 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.097 0.048 199.7 64: (ns/day) (hour/ns) 64: Performance: 8.916 2.692 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Pull group 1 'FirstWaterMolecule' has 3 atoms 64: Pull group 2 'SecondWaterMolecule' has 3 atoms 64: Number of degrees of freedom in T-Coupling group rest is 9.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Pull group natoms pbc atom distance at start reference at t=0 64: 1 3 2 64: 2 3 5 1.112 nm 1.000 nm 64: 64: There was 1 NOTE 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 4 steps, 0.0 ps. 64: Setting the LD random seed to -25690564 64: 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: turning H bonds into constraints... 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.106 0.053 199.7 64: (ns/day) (hour/ns) 64: Performance: 8.134 2.951 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 64: 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 64: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (152 ms) 64: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (153 ms total) 64: 64: [----------] 12 tests from FreezeWorks/FreezeGroupTest 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.195 0.098 199.8 64: (ns/day) (hour/ns) 64: Performance: 7.972 3.011 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (151 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.190 0.095 199.8 64: (ns/day) (hour/ns) 64: Performance: 8.184 2.933 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (150 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 11 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.255 0.128 199.9 64: (ns/day) (hour/ns) 64: Performance: 6.087 3.943 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (195 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.337 0.168 199.9 64: (ns/day) (hour/ns) 64: Performance: 4.618 5.197 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (240 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: NVE simulation: will use the initial temperature of 318.937 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 5 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.339 0.170 199.9 64: (ns/day) (hour/ns) 64: Performance: 4.580 5.240 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (242 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 64: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 64: Parrinello-Rahman is not implemented in md-vv. 64: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.258 0.129 199.9 64: (ns/day) (hour/ns) 64: Performance: 6.015 3.990 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (196 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.252 0.126 199.9 64: (ns/day) (hour/ns) 64: Performance: 6.171 3.889 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (188 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.278 0.139 199.9 64: (ns/day) (hour/ns) 64: Performance: 5.591 4.293 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (202 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.218 0.109 199.8 64: (ns/day) (hour/ns) 64: Performance: 7.139 3.362 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (216 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.168 0.084 199.9 64: (ns/day) (hour/ns) 64: Performance: 9.250 2.594 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (199 ms) 64: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: There are 5 atoms that are fully frozen and part of COMM removal 64: group(s), removing these atoms from the COMM removal group(s) 64: 64: 64: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: There are 3 atoms that are frozen along less then 3 dimensions and part 64: of COMM removal group(s), due to limitations in the code these still 64: contribute to the mass of the COM along frozen dimensions and therefore 64: the COMM correction will be too small. 64: 64: Number of degrees of freedom in T-Coupling group System is 25.50 64: 64: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 4 NOTEs 64: 64: There was 1 WARNING 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 64: 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Alanine-dipeptide' 64: 8 steps, 0.0 ps. 64: Generated 2145 of the 2145 non-bonded parameter combinations 64: 64: Generated 2145 of the 2145 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 64: 64: turning H bonds into constraints... 64: 64: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 64: 64: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.212 0.106 199.9 64: (ns/day) (hour/ns) 64: Performance: 7.324 3.277 64: 64: 64: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (220 ms) 64: [----------] 12 tests from FreezeWorks/FreezeGroupTest (2203 ms total) 64: 64: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -222876689 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.108 0.054 199.8 64: (ns/day) (hour/ns) 64: Performance: 28.665 0.837 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (69 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because verlet-buffer-tolerance is not set or used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -541081605 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.116 0.058 199.7 64: (ns/day) (hour/ns) 64: Performance: 26.843 0.894 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (75 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -21139977 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.162 0.081 199.8 64: (ns/day) (hour/ns) 64: Performance: 19.149 1.253 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (98 ms) 64: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 64: that with the Verlet scheme, nstlist has no effect on the accuracy of 64: your simulation. 64: 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 64: < 0 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (4) 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 64: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 64: Net Acceleration in X direction, will not be corrected 64: Net Acceleration in Y direction, will not be corrected 64: Net Acceleration in Z direction, will not be corrected 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 64: Can not increase nstlist because verlet-buffer-tolerance is not set or used 64: Using 1 MPI thread 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'spc2' 64: 8 steps, 0.0 ps. 64: Generated 3 of the 3 non-bonded parameter combinations 64: 64: Generated 3 of the 3 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: Setting gen_seed to -1209016890 64: 64: Velocities were taken from a Maxwell distribution at 0 K 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 12 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.163 0.082 199.8 64: (ns/day) (hour/ns) 64: Performance: 19.070 1.259 64: 64: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (97 ms) 64: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (341 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 28 tests from 7 test suites ran. (9167 ms total) 64: [ PASSED ] 27 tests. 64: [ SKIPPED ] 1 test, listed below: 64: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 64/87 Test #64: MdrunTestsOneRank ......................... Passed 9.23 sec test 65 Start 65: MdrunTestsTwoRanks 65: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunTestsTwoRanks.xml" 65: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 28 tests from 7 test suites. 65: [----------] Global test environment set-up. 65: [----------] 1 test from CompelTest 65: [ RUN ] CompelTest.SwapCanRun 65: Generating 1-4 interactions: fudge = 0.5 65: Split0 group 'Ch0' contains 83 atoms. 65: Split1 group 'Ch1' contains 83 atoms. 65: Solvent group 'SOL' contains 11931 atoms. 65: Swap group 'NA+' contains 19 atoms. 65: Swap group 'CL-' contains 19 atoms. 65: Number of degrees of freedom in T-Coupling group System is 27869.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 65: Removing center of mass motion in the presence of position restraints 65: might cause artifacts. When you are using position restraints to 65: equilibrate a macro-molecule, the artifacts are usually negligible. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Update groups can not be used for this system because there are three or more consecutively coupled constraints 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: SWAP: Determining initial numbers of ions per compartment. 65: SWAP: Setting pointers for checkpoint writing 65: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 65: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 65: starting mdrun 'Channel_coco in octane membrane' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -18878561 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein' 65: 65: turning all bonds into constraints... 65: 65: Excluding 3 bonded neighbours molecule type 'OCT' 65: 65: turning all bonds into constraints... 65: 65: Excluding 1 bonded neighbours molecule type 'NA' 65: 65: turning all bonds into constraints... 65: 65: Excluding 1 bonded neighbours molecule type 'CL' 65: 65: turning all bonds into constraints... 65: 65: Excluding 3 bonded neighbours molecule type 'Protein' 65: 65: Excluding 3 bonded neighbours molecule type 'OCT' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning all bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 1 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 12.6%. 65: The balanceable part of the MD step is 19%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 2.5%. 65: 65: 65: NOTE: 36 % of the run time was spent in domain decomposition, 65: 9 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 7.044 1.808 389.5 65: (ns/day) (hour/ns) 65: Performance: 0.717 33.487 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 65: 65: Update groups can not be used for this system because there are three or more consecutively coupled constraints 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: SWAP: Setting pointers for checkpoint writing 65: SWAP: Copying channel fluxes from checkpoint file data 65: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 65: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 65: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 65: starting mdrun 'Channel_coco in octane membrane' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 5.672 1.456 389.6 65: (ns/day) (hour/ns) 65: Performance: 0.890 26.963 65: [ OK ] CompelTest.SwapCanRun (9380 ms) 65: [----------] 1 test from CompelTest (9380 ms total) 65: 65: [----------] 6 tests from BondedInteractionsTest 65: [ RUN ] BondedInteractionsTest.NormalBondWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 2 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 52 % of the run time was spent in domain decomposition, 65: 10 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.291 0.073 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.186 20.244 65: Setting the LD random seed to -18350161 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalBondWorks (813 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 2 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 49 % of the run time was spent in domain decomposition, 65: 8 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 25 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.549 0.166 329.8 65: (ns/day) (hour/ns) 65: Performance: 0.519 46.245 65: Setting the LD random seed to -136253761 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedBondWorks (650 ms) 65: [ RUN ] BondedInteractionsTest.NormalAngleWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 85 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 5 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.377 0.628 378.4 65: (ns/day) (hour/ns) 65: Performance: 0.138 174.544 65: Setting the LD random seed to -8257 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalAngleWorks (2444 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 81 % of the run time was spent in domain decomposition, 65: 11 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.239 0.060 399.8 65: (ns/day) (hour/ns) 65: Performance: 1.444 16.620 65: Setting the LD random seed to -580931870 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (711 ms) 65: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 85 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.740 0.477 365.2 65: (ns/day) (hour/ns) 65: Performance: 0.181 132.372 65: Setting the LD random seed to -89653515 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.NormalDihedralWorks (1640 ms) 65: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 65: In moleculetype 'butane' 4 atoms are not bound by a potential or 65: constraint to any other atom in the same moleculetype. Although 65: technically this might not cause issues in a simulation, this often means 65: that the user forgot to add a bond/potential/constraint or put multiple 65: molecules in the same moleculetype definition by mistake. Run with -v to 65: get information for each atom. 65: 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 65: NVE simulation with an initial temperature of zero: will use a Verlet 65: buffer of 10%. Check your energy drift! 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 65: 65: Reading frames from gro file 'A single butane', 4 atoms. 65: Reading frame 0 time 0.000 Last frame 0 time 0.000 65: 65: NOTE: 86 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.029 0.535 379.1 65: (ns/day) (hour/ns) 65: Performance: 0.161 148.663 65: Setting the LD random seed to -537957442 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'butane' 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (2044 ms) 65: [----------] 6 tests from BondedInteractionsTest (8305 ms total) 65: 65: [----------] 2 tests from BoxDeformationTest 65: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (10) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Number of degrees of freedom in T-Coupling group rest is 33.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 0 steps, 0.0 ps. 65: 65: NOTE: 65 % of the run time was spent in domain decomposition, 65: 4 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 16 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.634 0.176 360.1 65: (ns/day) (hour/ns) 65: Performance: 0.982 24.442 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 1610562927 65: 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Setting gen_seed to -6324577 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (912 ms) 65: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (10) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group rest is 1293.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 20 steps, 0.0 ps. 65: Setting the LD random seed to -841683467 65: 65: Generated 330891 of the 330891 non-bonded parameter combinations 65: 65: Generated 330891 of the 330891 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 65: 65: Estimate for the relative computational load of the PME mesh part: 0.18 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 4.5%. 65: The balanceable part of the MD step is 11%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.5%. 65: 65: 65: Core t (s) Wall t (s) (%) 65: Time: 17.784 4.510 394.3 65: (ns/day) (hour/ns) 65: Performance: 0.805 29.828 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (7155 ms) 65: [----------] 2 tests from BoxDeformationTest (8068 ms total) 65: 65: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -1091568142 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.824 0.956 400.0 65: (ns/day) (hour/ns) 65: Performance: 0.452 53.117 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 2078252988 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 17 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 9 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 5.144 1.328 387.4 65: (ns/day) (hour/ns) 65: Performance: 0.325 73.776 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (double precision) 65: 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (4695 ms) 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 133036023 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.368 1.092 400.0 65: (ns/day) (hour/ns) 65: Performance: 0.396 60.675 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 2 [file ala.top, line 256]: 65: For energy conservation with LINCS, lincs_iter should be 2 or larger. 65: 65: 65: Number of degrees of freedom in T-Coupling group rest is 54.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 65: The optimal PME mesh load for parallel simulations is below 0.5 65: and for highly parallel simulations between 0.25 and 0.33, 65: for higher performance, increase the cut-off and the PME grid spacing. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'UNNAMED in water' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 2147178167 65: 65: Generated 2211 of the 2211 non-bonded parameter combinations 65: 65: Generated 2211 of the 2211 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 65: 65: turning H bonds into constraints... 65: 65: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 65: Calculating fourier grid dimensions for X Y Z 65: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 65: 65: Estimate for the relative computational load of the PME mesh part: 0.94 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 17 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.439 0.860 400.0 65: (ns/day) (hour/ns) 65: Performance: 0.502 47.766 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (3107 ms) 65: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (7804 ms total) 65: 65: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 65: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to 2145230712 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 8 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.184 0.836 380.9 65: (ns/day) (hour/ns) 65: Performance: 0.517 46.443 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 65: Can not increase nstlist because an NVE ensemble is used 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Setting the LD random seed to -1150386177 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 13 % of the run time was spent in domain decomposition, 65: 0 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 11 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 4.247 1.114 381.3 65: (ns/day) (hour/ns) 65: Performance: 0.388 61.871 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 65: 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (4592 ms) 65: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (4592 ms total) 65: 65: [----------] 12 tests from FreezeWorks/FreezeGroupTest 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 23.8%. 65: The balanceable part of the MD step is 42%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 10.1%. 65: 65: NOTE: 10.1 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 15 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 15 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.913 0.766 380.3 65: (ns/day) (hour/ns) 65: Performance: 1.015 23.641 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (1264 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 31.1%. 65: The balanceable part of the MD step is 39%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 12.3%. 65: 65: NOTE: 12.3 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 19 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.712 0.738 367.4 65: (ns/day) (hour/ns) 65: Performance: 1.054 22.777 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (1483 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 39.3%. 65: The balanceable part of the MD step is 40%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 15.5%. 65: 65: NOTE: 15.5 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 22 % of the run time was spent in domain decomposition, 65: 2 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 14 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.290 0.573 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.358 17.671 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (1243 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 7.3%. 65: The balanceable part of the MD step is 57%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 4.1%. 65: 65: 65: NOTE: 15 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 5.432 1.360 399.4 65: (ns/day) (hour/ns) 65: Performance: 0.572 41.969 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (2059 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: NVE simulation: will use the initial temperature of 318.937 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 13.8%. 65: The balanceable part of the MD step is 55%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 7.6%. 65: 65: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 65: in the domain decomposition. 65: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 65: You can also consider manually changing the decomposition (option -dd); 65: e.g. by using fewer domains along the box dimension in which there is 65: considerable inhomogeneity in the simulated system. 65: 65: NOTE: 18 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 33 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.841 0.992 387.2 65: (ns/day) (hour/ns) 65: Performance: 0.784 30.616 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (1567 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 65: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 65: Parrinello-Rahman is not implemented in md-vv. 65: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in domain decomposition, 65: 3 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 7 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.369 0.592 399.9 65: (ns/day) (hour/ns) 65: Performance: 1.313 18.285 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (2021 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 14 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 10 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.136 0.562 380.2 65: (ns/day) (hour/ns) 65: Performance: 1.384 17.345 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (1079 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 20, rlist from 0.756 to 0.861 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 14 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.146 0.812 387.4 65: (ns/day) (hour/ns) 65: Performance: 0.958 25.063 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (2391 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.641 0.942 386.6 65: (ns/day) (hour/ns) 65: Performance: 0.826 29.070 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (2415 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 9 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.340 0.337 397.7 65: (ns/day) (hour/ns) 65: Performance: 2.308 10.396 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (795 ms) 65: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: There are 5 atoms that are fully frozen and part of COMM removal 65: group(s), removing these atoms from the COMM removal group(s) 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: There are 3 atoms that are frozen along less then 3 dimensions and part 65: of COMM removal group(s), due to limitations in the code these still 65: contribute to the mass of the COM along frozen dimensions and therefore 65: the COMM correction will be too small. 65: 65: Number of degrees of freedom in T-Coupling group System is 25.50 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: There was 1 WARNING 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Changing nstlist from 8 to 100, rlist from 0.735 to 0.832 65: 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 17 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.192 0.312 382.7 65: (ns/day) (hour/ns) 65: Performance: 2.496 9.615 65: 65: 65: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (752 ms) 65: [----------] 12 tests from FreezeWorks/FreezeGroupTest (17076 ms total) 65: 65: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -14352 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 0.5%. 65: The balanceable part of the MD step is 32%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.2%. 65: 65: 65: NOTE: 21 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 10 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 3.480 0.902 385.8 65: (ns/day) (hour/ns) 65: Performance: 1.724 13.918 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (2468 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because verlet-buffer-tolerance is not set or used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to 1873802975 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 3.9%. 65: The balanceable part of the MD step is 43%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 1.7%. 65: 65: 65: NOTE: 24 % of the run time was spent in domain decomposition, 65: 3 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 6 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.677 0.669 399.9 65: (ns/day) (hour/ns) 65: Performance: 2.323 10.330 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (1023 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to 2136976625 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 0.8%. 65: The balanceable part of the MD step is 37%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 0.3%. 65: 65: 65: NOTE: 15 % of the run time was spent in domain decomposition, 65: 1 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: NOTE: 24 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 5.144 1.320 389.7 65: (ns/day) (hour/ns) 65: Performance: 1.178 20.369 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (2811 ms) 65: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 65: < 0 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 65: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 65: Net Acceleration in X direction, will not be corrected 65: Net Acceleration in Y direction, will not be corrected 65: Net Acceleration in Z direction, will not be corrected 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 65: Can not increase nstlist because verlet-buffer-tolerance is not set or used 65: Using 2 MPI threads 65: Using 2 OpenMP threads per tMPI thread 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Setting gen_seed to -16706 65: 65: Velocities were taken from a Maxwell distribution at 0 K 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: 65: Dynamic load balancing report: 65: DLB was off during the run due to low measured imbalance. 65: Average load imbalance: 4.6%. 65: The balanceable part of the MD step is 49%, load imbalance is computed from this. 65: Part of the total run time spent waiting due to load imbalance: 2.2%. 65: 65: 65: NOTE: 22 % of the run time was spent communicating energies, 65: you might want to increase some nst* mdp options 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.857 0.464 399.9 65: (ns/day) (hour/ns) 65: Performance: 3.349 7.166 65: 65: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (587 ms) 65: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (6891 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 28 tests from 7 test suites ran. (62331 ms total) 65: [ PASSED ] 27 tests. 65: [ SKIPPED ] 1 test, listed below: 65: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 65/87 Test #65: MdrunTestsTwoRanks ........................ Passed 62.41 sec test 66 Start 66: MdrunSingleRankAlgorithmsTests 66: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 66: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 5 tests from 3 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from DispersionCorrectionTest 66: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 30.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 66: There are 9 non-linear virtual site constructions. Their contribution to 66: the energy error is approximated. In most cases this does not affect the 66: error significantly. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 66: Changing nstlist from 10 to 40, rlist from 1.027 to 1.175 66: 66: Update groups can not be used for this system because an incompatible virtual site type is used 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine dipeptide in vacuo' 66: 200 steps, 0.4 ps. 66: Setting the LD random seed to -16843793 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 66: 66: turning H bonds into constraints... 66: 66: Cleaning up constraints and constant bonded interactions with virtual sites 66: 66: Converted 3 Bonds with virtual sites to connections, 7 left 66: 66: Removed 18 Angles with virtual sites, 21 left 66: 66: Removed 10 Proper Dih.s with virtual sites, 44 left 66: 66: Converted 12 Constraints with virtual sites to connections, 0 left 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.234 0.117 199.9 66: (ns/day) (hour/ns) 66: Performance: 297.215 0.081 66: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (307 ms) 66: [----------] 1 test from DispersionCorrectionTest (307 ms total) 66: 66: [----------] 1 test from OriresTest 66: [ RUN ] OriresTest.OriresCanRun 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group System is 518.00 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 66: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank. 66: Changing nstlist from 10 to 25, rlist from 1.076 to 1.219 66: 66: 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 66: 10 steps, 0.0 ps. 66: Setting the LD random seed to 2071916415 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.267 0.133 199.9 66: (ns/day) (hour/ns) 66: Performance: 14.254 1.684 66: [ OK ] OriresTest.OriresCanRun (1289 ms) 66: [----------] 1 test from OriresTest (1289 ms total) 66: 66: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 66: Number of degrees of freedom in T-Coupling group rest is 10.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Dipoles' 66: 20 steps, 0.1 ps. 66: Setting the LD random seed to 2013216353 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Dipole' 66: 66: Searching the wall atom type(s) 66: 66: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 66: 66: Estimate for the relative computational load of the PME mesh part: 1.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.941 0.471 200.0 66: (ns/day) (hour/ns) 66: Performance: 9.635 2.491 66: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (double precision) 66: 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (544 ms) 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 66: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 66: The supported numbers are > 1. 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 66: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: With epsilon_surface > 0 all molecules should be neutral. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: With epsilon_surface > 0 you can only use domain decomposition when there 66: are only small molecules with all bonds constrained (mdrun will check for 66: this). 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 4 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI thread 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Dipoles' 66: 20 steps, 0.1 ps. 66: Setting the LD random seed to -38920 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Dipole' 66: 66: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 66: 66: Estimate for the relative computational load of the PME mesh part: 1.00 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 1.149 0.574 200.0 66: (ns/day) (hour/ns) 66: Performance: 7.896 3.040 66: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as double precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 66: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (621 ms) 66: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (1165 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 5 tests from 3 test suites ran. (2852 ms total) 66: [ PASSED ] 5 tests. 66/87 Test #66: MdrunSingleRankAlgorithmsTests ............ Passed 2.92 sec test 67 Start 67: Minimize1RankTests 67: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Minimize1RankTests.xml" 67: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 12 tests from 2 test suites. 67: [----------] Global test environment set-up. 67: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -4.79910463671092e+01 67: Maximum force = 1.86297359432231e+02 on atom 13 67: Norm of force = 8.77219865482157e+01 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (989 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 3.02331e+02 on atom 3 67: F-Norm = 1.18024e+02 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -5.58622538633302e+01 67: Maximum force = 4.27274822366368e+02 on atom 13 67: Norm of force = 1.84530029253754e+02 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1539 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 22.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 3.19376899751523e+02 67: Maximum force = 9.99884921009767e+03 on atom 9 67: Norm of force = 4.61669565054298e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (242 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: 67: NOTE 3 [file glycine_vacuo.top, line 12]: 67: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 67: 67: Number of degrees of freedom in T-Coupling group System is 22.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 5 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 2.41575e+04 on atom 10 67: F-Norm = 1.18451e+04 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 1.51743018140928e+02 67: Maximum force = 7.42089573409108e+03 on atom 9 67: Norm of force = 3.56929298615740e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: turning H bonds into constraints... 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (231 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file unknown]: 67: You are using constraints on all bonds, whereas the forcefield has been 67: parametrized only with constraints involving hydrogen atoms. We suggest 67: using constraints = h-bonds instead, this will also improve performance. 67: 67: Number of degrees of freedom in T-Coupling group System is 23.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 5 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Update groups can not be used for this system because an incompatible virtual site type is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.56984193848274e+02 67: Maximum force = 4.56923624626570e+02 on atom 17 67: Norm of force = 1.83258377168389e+02 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 67: 67: turning all bonds into constraints... 67: 67: Cleaning up constraints and constant bonded interactions with virtual sites 67: 67: Removed 18 Angles with virtual sites, 21 left 67: 67: Removed 10 Proper Dih.s with virtual sites, 44 left 67: 67: Converted 15 Constraints with virtual sites to connections, 7 left 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (195 ms) 67: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file unknown]: 67: You are using constraints on all bonds, whereas the forcefield has been 67: parametrized only with constraints involving hydrogen atoms. We suggest 67: using constraints = h-bonds instead, this will also improve performance. 67: 67: 67: NOTE 4 [file unknown]: 67: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 67: 67: Number of degrees of freedom in T-Coupling group System is 23.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 6 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Update groups can not be used for this system because an incompatible virtual site type is used 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 1.06800e+03 on atom 28 67: F-Norm = 4.26922e+02 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = -1.69410778678181e+02 67: Maximum force = 2.18225948473987e+02 on atom 17 67: Norm of force = 7.92068036537548e+01 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 67: 67: turning all bonds into constraints... 67: 67: Cleaning up constraints and constant bonded interactions with virtual sites 67: 67: Removed 18 Angles with virtual sites, 21 left 67: 67: Removed 10 Proper Dih.s with virtual sites, 44 left 67: 67: Converted 15 Constraints with virtual sites to connections, 7 left 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (276 ms) 67: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3474 ms total) 67: 67: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents converged to Fmax < 10 in 1 steps 67: Potential Energy = -9.74257075835447e-01 67: Maximum force = 4.01322929015133e+00 on atom 1 67: Norm of force = 1.63839399694378e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (37 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 4.01323e+00 on atom 1 67: F-Norm = 1.63839e+00 67: 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 67: Potential Energy = -9.90642313893957e-01 67: Maximum force = 2.57812909491104e+00 on atom 1 67: Norm of force = 1.05251679559258e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (34 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 67: 67: Number of degrees of freedom in T-Coupling group System is 33.00 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 3 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Low-Memory BFGS Minimizer: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: Using 10 BFGS correction steps. 67: 67: F-max = 4.01323e+00 on atom 1 67: F-Norm = 1.63839e+00 67: 67: 67: writing lowest energy coordinates. 67: 67: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 67: Potential Energy = -9.90642313893957e-01 67: Maximum force = 2.57812909491104e+00 on atom 1 67: Norm of force = 1.05251679559258e+00 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (37 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Steepest Descents: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Steepest Descents did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 3.19395484891520e+02 67: Maximum force = 9.97041707197911e+03 on atom 9 67: Norm of force = 4.62274878665467e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (142 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Polak-Ribiere Conjugate Gradients: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: F-max = 2.41672e+04 on atom 10 67: F-Norm = 1.19357e+04 67: 67: 67: Energy minimization reached the maximum number of steps before the forces 67: reached the requested precision Fmax < 10. 67: 67: writing lowest energy coordinates. 67: 67: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 67: Potential Energy = 1.56258793899480e+02 67: Maximum force = 7.50181017480397e+03 on atom 9 67: Norm of force = 3.61390332564874e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (215 ms) 67: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 67: setting nstcomm equal to nstcalcenergy for less overhead 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 67: 67: Generating 1-4 interactions: fudge = 1 67: Number of degrees of freedom in T-Coupling group System is 27.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 67: COM removal frequency is set to (4). 67: Other settings require a global communication frequency of 100. 67: Note that this will require additional global communication steps, 67: which will reduce performance when using multiple ranks. 67: Consider setting nstcomm to a multiple of 100. 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 67: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 67: 67: Using 1 MPI thread 67: Using 2 OpenMP threads 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: 67: Low-Memory BFGS Minimizer: 67: Tolerance (Fmax) = 1.00000e+01 67: Number of steps = 4 67: Using 10 BFGS correction steps. 67: 67: F-max = 2.41672e+04 on atom 10 67: F-Norm = 1.19357e+04 67: 67: 67: Energy minimization has stopped, but the forces have not converged to the 67: requested precision Fmax < 10 (which may not be possible for your system). It 67: stopped because the algorithm tried to make a new step whose size was too 67: small, or there was no change in the energy since last step. Either way, we 67: regard the minimization as converged to within the available machine 67: precision, given your starting configuration and EM parameters. 67: 67: writing lowest energy coordinates. 67: 67: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 67: but did not reach the requested Fmax < 10. 67: Potential Energy = 5.61116097794205e+02 67: Maximum force = 1.26854826291223e+04 on atom 10 67: Norm of force = 6.06436286976271e+03 67: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 67: 67: Generated 17396 of the 20503 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Glycine' 67: 67: This run will generate roughly 0 Mb of data 67: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (136 ms) 67: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (603 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 12 tests from 2 test suites ran. (4121 ms total) 67: [ PASSED ] 12 tests. 67/87 Test #67: Minimize1RankTests ........................ Passed 4.16 sec test 68 Start 68: Minimize2RankTests 68: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/minimize-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/Minimize2RankTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 12 tests from 2 test suites. 68: [----------] Global test environment set-up. 68: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -4.79910463671093e+01 68: Maximum force = 1.86297359432232e+02 on atom 13 68: Norm of force = 8.77219865482159e+01 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (3869 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 3.02331e+02 on atom 3 68: F-Norm = 1.18024e+02 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -5.58622538633302e+01 68: Maximum force = 4.27274822366367e+02 on atom 13 68: Norm of force = 1.84530029253753e+02 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 330891 of the 330891 non-bonded parameter combinations 68: 68: Generated 330891 of the 330891 1-4 parameter combinations 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (3283 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 22.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 3.19376899751523e+02 68: Maximum force = 9.99884921009767e+03 on atom 9 68: Norm of force = 4.61669565054298e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: turning H bonds into constraints... 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1400 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: 68: NOTE 3 [file glycine_vacuo.top, line 12]: 68: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 68: 68: Number of degrees of freedom in T-Coupling group System is 22.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 2.41575e+04 on atom 10 68: F-Norm = 1.18451e+04 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 1.51743018140927e+02 68: Maximum force = 7.42089573409111e+03 on atom 9 68: Norm of force = 3.56929298615739e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: turning H bonds into constraints... 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (2495 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 5 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -1.56984193848274e+02 68: Maximum force = 4.56923624626570e+02 on atom 17 68: Norm of force = 1.83258377168389e+02 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (1935 ms) 68: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 0.5 68: 68: NOTE 3 [file unknown]: 68: You are using constraints on all bonds, whereas the forcefield has been 68: parametrized only with constraints involving hydrogen atoms. We suggest 68: using constraints = h-bonds instead, this will also improve performance. 68: 68: 68: NOTE 4 [file unknown]: 68: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 68: 68: Number of degrees of freedom in T-Coupling group System is 23.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 6 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 1.06800e+03 on atom 28 68: F-Norm = 4.26922e+02 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = -1.69410778678181e+02 68: Maximum force = 2.18225948473987e+02 on atom 17 68: Norm of force = 7.92068036537548e+01 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning all bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 15 Constraints with virtual sites to connections, 7 left 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (2843 ms) 68: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (15829 ms total) 68: 68: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents converged to Fmax < 10 in 1 steps 68: Potential Energy = -9.74257075835447e-01 68: Maximum force = 4.01322929015133e+00 on atom 3 68: Norm of force = 1.63839399694378e+00 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1021 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 4.01323e+00 on atom 3 68: F-Norm = 1.63839e+00 68: 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 68: Potential Energy = -9.90642313893957e-01 68: Maximum force = 2.57812909491104e+00 on atom 3 68: Norm of force = 1.05251679559258e+00 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (771 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 68: 68: Number of degrees of freedom in T-Coupling group System is 33.00 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 3 NOTEs 68: 68: There was 1 WARNING 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Argon' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Steepest Descents: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Steepest Descents did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 3.19395484891520e+02 68: Maximum force = 9.97041707197911e+03 on atom 9 68: Norm of force = 4.62274878665467e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3325 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 68: Using 2 MPI threads 68: Using 2 OpenMP threads per tMPI thread 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: 68: Polak-Ribiere Conjugate Gradients: 68: Tolerance (Fmax) = 1.00000e+01 68: Number of steps = 4 68: F-max = 2.41672e+04 on atom 10 68: F-Norm = 1.19357e+04 68: 68: 68: Energy minimization reached the maximum number of steps before the forces 68: reached the requested precision Fmax < 10. 68: 68: writing lowest energy coordinates. 68: 68: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 68: Potential Energy = 1.56258793899480e+02 68: Maximum force = 7.50181017480397e+03 on atom 9 68: Norm of force = 3.61390332564874e+03 68: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (2875 ms) 68: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 68: that with the Verlet scheme, nstlist has no effect on the accuracy of 68: your simulation. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 68: setting nstcomm equal to nstcalcenergy for less overhead 68: 68: 68: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 68: 68: Generating 1-4 interactions: fudge = 1 68: Number of degrees of freedom in T-Coupling group System is 27.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 68: COM removal frequency is set to (4). 68: Other settings require a global communication frequency of 100. 68: Note that this will require additional global communication steps, 68: which will reduce performance when using multiple ranks. 68: Consider setting nstcomm to a multiple of 100. 68: 68: 68: There were 4 NOTEs 68: 68: There was 1 WARNING 68: Generated 20503 of the 20503 non-bonded parameter combinations 68: 68: Generated 17396 of the 20503 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Glycine' 68: 68: This run will generate roughly 0 Mb of data 68: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (272 ms) 68: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (8288 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 12 tests from 2 test suites ran. (24154 ms total) 68: [ PASSED ] 12 tests. 68/87 Test #68: Minimize2RankTests ........................ Passed 24.19 sec test 69 Start 69: MdrunNonIntegratorTests 69: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 53 tests from 5 test suites. 69: [----------] Global test environment set-up. 69: [----------] 1 test from NonbondedBenchTest 69: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 69: SIMD width: 2 69: System size: 3000 atoms 69: Cut-off radius: 1 nm 69: Number of threads: 1 69: Number of iterations: 1 69: Compute energies: no 69: Ewald excl. corr.: analytical 69: 69: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 69: total useful 69: Ewald all geom. 4xM 0.573 0.5735 1.8477 1.0981 69: [ OK ] NonbondedBenchTest.BasicEndToEndTest (68 ms) 69: [----------] 1 test from NonbondedBenchTest (78 ms total) 69: 69: [----------] 5 tests from NormalModesWorks/NormalModesTest 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 15.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=6), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation '2 scaled waters' 69: 12 steps. 69: 69: Maximum force: 9.96989e-06 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 18... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--18 to eigenvec.trr 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Generated 3 of the 3 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: This run will generate roughly 0 Mb of data 69: There are: 6 Atoms 69: Using begin = 7 and end = 18 69: Full matrix storage format, nrow=18, ncols=18 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (347 ms) 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 1 69: 69: NOTE 3 [file villin.top, line 2452]: 69: System has non-zero total charge: -2.000000 69: Total charge should normally be an integer. See 69: https://manual.gromacs.org/current/user-guide/floating-point.html 69: for discussion on how close it should be to an integer. 69: 69: 69: 69: Number of degrees of freedom in T-Coupling group System is 765.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=256), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN' 69: 512 steps. 69: 69: Maximum force: 6.97568e-04 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 50... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--50 to eigenvec.trr 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 69: 69: This run will generate roughly 0 Mb of data 69: There are: 256 Atoms 69: Using begin = 7 and end = 50 69: Full matrix storage format, nrow=768, ncols=768 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (17103 ms) 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 15.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=6), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation 'flex spc dimer' 69: 12 steps. 69: 69: Maximum force: 3.36401e-04 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 18... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--18 to eigenvec.trr 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: This run will generate roughly 0 Mb of data 69: There are: 6 Atoms 69: Using begin = 7 and end = 18 69: Full matrix storage format, nrow=18, ncols=18 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (2120 ms) 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 6.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=3), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation '1 TIP5P' 69: 6 steps. 69: 69: Maximum force: 2.42882e-04 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 9... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--9 to eigenvec.trr 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: This run will generate roughly 0 Mb of data 69: There are: 3 Atoms 69: There are: 2 VSites 69: Using begin = 7 and end = 9 69: Full matrix storage format, nrow=9, ncols=9 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (1712 ms) 69: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: Number of degrees of freedom in T-Coupling group System is 15.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Update groups can not be used for this system because the construction atoms of a virtual site are only partly with a group of constrained atoms 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Small system size (N=6), using full Hessian format. 69: Allocating Hessian memory... 69: 69: starting normal mode calculation 'sw dimer' 69: 12 steps. 69: 69: Maximum force: 1.07599e-03 69: The force is probably not small enough to ensure that you are at a minimum. 69: Be aware that negative eigenvalues may occur 69: when the resulting matrix is diagonalized. 69: 69: 69: Writing Hessian... 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Reading double precision matrix generated by GROMACS 2024.4-Debian_2024.4_1 69: 69: Diagonalizing to find vectors 7 through 18... 69: Writing eigenvalues... 69: 69: Writing average structure & eigenvectors 7--18 to eigenvec.trr 69: Generated 6 of the 10 non-bonded parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SW' 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: This run will generate roughly 0 Mb of data 69: There are: 6 Atoms 69: There are: 2 Shells 69: There are: 2 VSites 69: 69: NOTE: in the current version shell prediction during the crun is disabled 69: 69: Using begin = 7 and end = 18 69: Full matrix storage format, nrow=18, ncols=18 69: Writing eigenfrequencies - negative eigenvalues will be set to zero. 69: Cannot compute entropy when -first = 7 69: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (654 ms) 69: [----------] 5 tests from NormalModesWorks/NormalModesTest (21938 ms total) 69: 69: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 13 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.223 0.111 199.9 69: (ns/day) (hour/ns) 69: Performance: 13.174 1.822 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 69: 69: trr version: GMX_trn_file (double precision) 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 50 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.059 0.030 199.8 69: (ns/day) (hour/ns) 69: Performance: 49.469 0.485 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (173 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 68.810 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 11 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.271 0.136 199.9 69: (ns/day) (hour/ns) 69: Performance: 10.818 2.219 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 45 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.081 0.040 199.8 69: (ns/day) (hour/ns) 69: Performance: 36.350 0.660 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (203 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.246 0.123 199.9 69: (ns/day) (hour/ns) 69: Performance: 11.928 2.012 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.712 to 0.746 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 46 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.074 0.037 199.8 69: (ns/day) (hour/ns) 69: Performance: 39.496 0.608 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (194 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: There were 2 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Argon' 69: 16 steps, 0.0 ps. 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.190 0.095 199.9 69: (ns/day) (hour/ns) 69: Performance: 15.426 1.556 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 40 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.052 0.026 199.7 69: (ns/day) (hour/ns) 69: Performance: 56.584 0.424 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (141 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 398.997 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.292 0.146 199.9 69: (ns/day) (hour/ns) 69: Performance: 10.050 2.388 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 54 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.090 0.045 199.9 69: (ns/day) (hour/ns) 69: Performance: 32.449 0.740 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2031 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: NVE simulation: will use the initial temperature of 398.997 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.406 0.203 200.0 69: (ns/day) (hour/ns) 69: Performance: 7.236 3.317 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 49 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.060 0.030 199.8 69: (ns/day) (hour/ns) 69: Performance: 48.582 0.494 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (1737 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.186 0.093 199.9 69: (ns/day) (hour/ns) 69: Performance: 15.811 1.518 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 100, rlist from 0.736 to 0.834 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 46 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.041 0.021 199.6 69: (ns/day) (hour/ns) 69: Performance: 71.013 0.338 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (994 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'spc2' 69: 16 steps, 0.0 ps. 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.302 0.151 199.9 69: (ns/day) (hour/ns) 69: Performance: 9.729 2.467 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 42 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.072 0.036 199.8 69: (ns/day) (hour/ns) 69: Performance: 40.713 0.589 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (719 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: NVE simulation: will use the initial temperature of 456.887 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 6 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.834 0.417 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.520 6.819 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 38 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.100 0.050 199.8 69: (ns/day) (hour/ns) 69: Performance: 29.333 0.818 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (560 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: NVE simulation: will use the initial temperature of 456.887 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 6 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.997 0.498 200.0 69: (ns/day) (hour/ns) 69: Performance: 2.947 8.144 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 43 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.101 0.051 199.9 69: (ns/day) (hour/ns) 69: Performance: 28.978 0.828 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (627 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.815 0.408 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.603 6.661 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 80, rlist from 0.75 to 0.871 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 33 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.151 0.076 199.9 69: (ns/day) (hour/ns) 69: Performance: 19.438 1.235 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (746 ms) 69: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: There are 9 non-linear virtual site constructions. Their contribution to 69: the energy error is approximated. In most cases this does not affect the 69: error significantly. 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'Alanine dipeptide in vacuo' 69: 16 steps, 0.0 ps. 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 2.144 1.072 200.0 69: (ns/day) (hour/ns) 69: Performance: 1.370 17.517 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 25, rlist from 0.73 to 0.814 69: 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 34 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.246 0.123 199.9 69: (ns/day) (hour/ns) 69: Performance: 11.915 2.014 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (1476 ms) 69: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (9619 ms total) 69: 69: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.659 0.330 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.454 5.388 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 46 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.065 0.033 199.7 69: (ns/day) (hour/ns) 69: Performance: 45.166 0.531 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (484 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.220 0.110 199.8 69: (ns/day) (hour/ns) 69: Performance: 13.312 1.803 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 43 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.051 0.026 199.6 69: (ns/day) (hour/ns) 69: Performance: 57.319 0.419 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (173 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.193 0.097 199.8 69: (ns/day) (hour/ns) 69: Performance: 15.207 1.578 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 42 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.057 0.028 199.6 69: (ns/day) (hour/ns) 69: Performance: 51.715 0.464 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (161 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.404 0.202 199.9 69: (ns/day) (hour/ns) 69: Performance: 7.270 3.301 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 50 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.121 0.060 199.9 69: (ns/day) (hour/ns) 69: Performance: 24.349 0.986 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (304 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.787 0.394 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.731 6.433 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 43 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.294 0.147 199.9 69: (ns/day) (hour/ns) 69: Performance: 10.000 2.400 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (640 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.000 0.500 200.0 69: (ns/day) (hour/ns) 69: Performance: 2.937 8.172 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 35 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.245 0.123 199.9 69: (ns/day) (hour/ns) 69: Performance: 11.975 2.004 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (792 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.812 0.406 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.618 6.634 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 47 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.218 0.109 199.9 69: (ns/day) (hour/ns) 69: Performance: 13.469 1.782 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (672 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: NOTE: 10 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.938 0.469 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.132 7.662 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 55 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.263 0.132 199.9 69: (ns/day) (hour/ns) 69: Performance: 11.149 2.153 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (743 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.793 0.397 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.704 6.479 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 56 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.225 0.113 199.9 69: (ns/day) (hour/ns) 69: Performance: 13.022 1.843 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (643 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.763 0.382 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.849 6.235 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 37 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.221 0.111 199.9 69: (ns/day) (hour/ns) 69: Performance: 13.285 1.807 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (636 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.861 0.431 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.412 7.035 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 26 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.238 0.119 199.9 69: (ns/day) (hour/ns) 69: Performance: 12.356 1.942 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (700 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.767 0.384 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.829 6.268 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 58 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.161 0.080 199.9 69: (ns/day) (hour/ns) 69: Performance: 18.271 1.314 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (583 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.842 0.421 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.488 6.881 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 81 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.207 0.103 199.9 69: (ns/day) (hour/ns) 69: Performance: 14.204 1.690 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (610 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.959 0.480 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.062 7.837 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 43 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.241 0.121 199.9 69: (ns/day) (hour/ns) 69: Performance: 12.176 1.971 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (718 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.023 0.512 200.0 69: (ns/day) (hour/ns) 69: Performance: 2.870 8.362 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 44 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.186 0.093 199.9 69: (ns/day) (hour/ns) 69: Performance: 15.770 1.522 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (731 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.949 0.475 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.095 7.756 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 42 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.216 0.108 199.9 69: (ns/day) (hour/ns) 69: Performance: 13.579 1.767 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (703 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.872 0.436 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.368 7.125 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 56 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.188 0.094 199.9 69: (ns/day) (hour/ns) 69: Performance: 15.641 1.534 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (646 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.823 0.412 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.568 6.727 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 54 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.138 0.069 199.8 69: (ns/day) (hour/ns) 69: Performance: 21.206 1.132 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (579 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.751 0.376 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.909 6.140 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 33 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.151 0.075 199.9 69: (ns/day) (hour/ns) 69: Performance: 19.498 1.231 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (529 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.700 0.350 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.195 5.721 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 37 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.156 0.078 199.9 69: (ns/day) (hour/ns) 69: Performance: 18.808 1.276 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (519 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.679 0.339 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.329 5.545 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 56 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.110 0.055 199.8 69: (ns/day) (hour/ns) 69: Performance: 26.665 0.900 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (475 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: NVE simulation: will use the initial temperature of 293.480 K for 69: determining the Verlet buffer size 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.627 0.313 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.687 5.121 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 40 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.125 0.063 199.9 69: (ns/day) (hour/ns) 69: Performance: 23.428 1.024 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (440 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.588 0.294 199.9 69: (ns/day) (hour/ns) 69: Performance: 4.991 4.809 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 27 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.123 0.062 199.8 69: (ns/day) (hour/ns) 69: Performance: 23.796 1.009 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (459 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.611 0.305 199.9 69: (ns/day) (hour/ns) 69: Performance: 4.809 4.991 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 61 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.133 0.067 199.9 69: (ns/day) (hour/ns) 69: Performance: 22.017 1.090 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (485 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.804 0.402 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.651 6.574 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 59 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.221 0.110 199.9 69: (ns/day) (hour/ns) 69: Performance: 13.313 1.803 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (638 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.892 0.446 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.292 7.289 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 39 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.201 0.101 199.9 69: (ns/day) (hour/ns) 69: Performance: 14.575 1.647 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (698 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.776 0.388 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.784 6.343 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 54 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.191 0.096 199.9 69: (ns/day) (hour/ns) 69: Performance: 15.365 1.562 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (620 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.807 0.404 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.638 6.597 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 38 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.197 0.098 199.9 69: (ns/day) (hour/ns) 69: Performance: 14.918 1.609 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (654 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.787 0.394 200.0 69: (ns/day) (hour/ns) 69: Performance: 3.731 6.433 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 27 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.188 0.094 199.9 69: (ns/day) (hour/ns) 69: Performance: 15.635 1.535 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (627 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.771 0.385 199.9 69: (ns/day) (hour/ns) 69: Performance: 3.812 6.297 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 44 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.180 0.090 199.9 69: (ns/day) (hour/ns) 69: Performance: 16.270 1.475 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (608 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.653 0.326 199.9 69: (ns/day) (hour/ns) 69: Performance: 4.500 5.333 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 32 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.174 0.087 199.9 69: (ns/day) (hour/ns) 69: Performance: 16.854 1.424 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (534 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.697 0.349 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.214 5.696 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 54 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.150 0.075 199.9 69: (ns/day) (hour/ns) 69: Performance: 19.617 1.223 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (565 ms) 69: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: Setting nstcalcenergy (100) equal to nstenergy (4) 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Number of degrees of freedom in T-Coupling group System is 79.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun '30 system in water' 69: 16 steps, 0.0 ps. 69: Generated 2485 of the 2485 non-bonded parameter combinations 69: 69: Generated 2485 of the 2485 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'nonanol' 69: 69: turning H bonds into constraints... 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: 69: turning H bonds into constraints... 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.690 0.345 200.0 69: (ns/day) (hour/ns) 69: Performance: 4.254 5.642 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Changing nstlist from 8 to 20, rlist from 0.759 to 0.868 69: 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 69: 69: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 69: 69: NOTE: 47 % of the run time was spent in pair search, 69: you might want to increase nstlist (this has no effect on accuracy) 69: 69: Core t (s) Wall t (s) (%) 69: Time: 0.173 0.087 199.9 69: (ns/day) (hour/ns) 69: Performance: 16.939 1.417 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 69: 69: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (559 ms) 69: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (18943 ms total) 69: 69: [----------] 2 tests from Angles1/SimpleMdrunTest 69: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file angles1.top, line 72]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group System is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]: 69: NVE simulation: will use the initial temperature of 238.919 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'This_incredible_box_of_butane' 69: 50 steps, 0.1 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.409 0.704 200.0 69: (ns/day) (hour/ns) 69: Performance: 6.256 3.836 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 69: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (746 ms) 69: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file angles1.top, line 72]: 69: In moleculetype 'butane' 4 atoms are not bound by a potential or 69: constraint to any other atom in the same moleculetype. Although 69: technically this might not cause issues in a simulation, this often means 69: that the user forgot to add a bond/potential/constraint or put multiple 69: molecules in the same moleculetype definition by mistake. Run with -v to 69: get information for each atom. 69: 69: Number of degrees of freedom in T-Coupling group System is 9.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]: 69: NVE simulation: will use the initial temperature of 238.919 K for 69: determining the Verlet buffer size 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 69: Can not increase nstlist because an NVE ensemble is used 69: Using 1 MPI thread 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: starting mdrun 'This_incredible_box_of_butane' 69: 50 steps, 0.1 ps. 69: Generated 3 of the 3 non-bonded parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'butane' 69: 69: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K 69: 69: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm 69: 69: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm 69: 69: Note that mdrun will redetermine rlist based on the actual pair-list setup 69: 69: This run will generate roughly 0 Mb of data 69: 69: Writing final coordinates. 69: 69: Core t (s) Wall t (s) (%) 69: Time: 1.757 0.879 200.0 69: (ns/day) (hour/ns) 69: Performance: 5.014 4.786 69: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 5 time 0.020 Reading energy frame 6 time 0.024 Reading energy frame 7 time 0.028 Reading energy frame 8 time 0.032 Reading energy frame 9 time 0.036 Reading energy frame 10 time 0.040 Reading energy frame 11 time 0.044 Reading energy frame 12 time 0.048 Reading energy frame 13 time 0.050 Last energy frame read 13 time 0.050 69: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (913 ms) 69: [----------] 2 tests from Angles1/SimpleMdrunTest (1673 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 53 tests from 5 test suites ran. (52366 ms total) 69: [ PASSED ] 53 tests. 69/87 Test #69: MdrunNonIntegratorTests ................... Passed 52.44 sec test 70 Start 70: MdrunTpiTests 70: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 2 tests from 1 test suite. 70: [----------] Global test environment set-up. 70: [----------] 2 tests from Simple/TpiTest 70: [ RUN ] Simple/TpiTest.ReproducesOutput/0 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 1308.00 70: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 70: TPI is not implemented for GPUs. 70: 70: Using 1 MPI thread 70: Using 1 OpenMP thread 70: 70: 70: NOTE: Thread affinity was not set. 70: Reading frames from gro file '216 water molecules', 648 atoms. 70: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 70: Last frame 0 time 0.000 70: Generated 331705 of the 331705 non-bonded parameter combinations 70: 70: Generated 331705 of the 331705 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Excluding 3 bonded neighbours molecule type 'methane' 70: Analysing residue names: 70: There are: 216 Water residues 70: There are: 1 Other residues 70: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1573 ms) 70: [ RUN ] Simple/TpiTest.ReproducesOutput/1 70: Generating 1-4 interactions: fudge = 0.5 70: Number of degrees of freedom in T-Coupling group System is 1308.00 70: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 70: TPI is not implemented for GPUs. 70: 70: Using 1 MPI thread 70: Using 1 OpenMP thread 70: 70: 70: NOTE: Thread affinity was not set. 70: Reading frames from gro file '216 water molecules', 648 atoms. 70: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 70: Last frame 0 time 0.000 70: Generated 331705 of the 331705 non-bonded parameter combinations 70: 70: Generated 331705 of the 331705 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: 70: Excluding 3 bonded neighbours molecule type 'methane' 70: Analysing residue names: 70: There are: 216 Water residues 70: There are: 1 Other residues 70: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] Simple/TpiTest.ReproducesOutput/1 (1280 ms) 70: [----------] 2 tests from Simple/TpiTest (2854 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 2 tests from 1 test suite ran. (2911 ms total) 70: [ PASSED ] 2 tests. 70/87 Test #70: MdrunTpiTests ............................. Passed 3.01 sec test 71 Start 71: MdrunMpiTests 71: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 16 tests from 2 test suites. 71: [----------] Global test environment set-up. 71: [----------] 4 tests from MimicTest 71: [ RUN ] MimicTest.OneQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 74 % of the run time was spent in domain decomposition, 71: 4 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: NOTE: 10 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.709 0.177 399.9 71: (ns/day) (hour/ns) 71: Performance: 0.487 49.237 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -219156547 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.OneQuantumMol (2006 ms) 71: [ RUN ] MimicTest.AllQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 73 % of the run time was spent in domain decomposition, 71: 5 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.646 0.161 399.9 71: (ns/day) (hour/ns) 71: Performance: 0.535 44.857 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -287318145 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.AllQuantumMol (1303 ms) 71: [ RUN ] MimicTest.TwoQuantumMol 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 21.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 71: 71: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 82 % of the run time was spent in domain decomposition, 71: 1 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: NOTE: 8 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 3.078 0.814 378.3 71: (ns/day) (hour/ns) 71: Performance: 0.106 226.072 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -17410 71: 71: Generated 10 of the 10 non-bonded parameter combinations 71: 71: Generated 10 of the 10 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.TwoQuantumMol (3076 ms) 71: [ RUN ] MimicTest.BondCuts 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: For a correct single-point energy evaluation with nsteps = 0, use 71: continuation = yes to avoid constraining the input coordinates. 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 66.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: NVE simulation: will use the initial temperature of 300.368 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 71: 71: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 71: Reading frame 0 time 0.000 Last frame 0 time 0.000 71: 71: NOTE: 67 % of the run time was spent in domain decomposition, 71: 5 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.916 0.229 400.0 71: (ns/day) (hour/ns) 71: Performance: 0.377 63.641 71: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 71: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -35128330 71: 71: Generated 2211 of the 2211 non-bonded parameter combinations 71: 71: Generated 2211 of the 2211 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: [ OK ] MimicTest.BondCuts (796 ms) 71: [----------] 4 tests from MimicTest (7195 ms total) 71: 71: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: There was 1 NOTE 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 9.00 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group rest is 9.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: NVE simulation with an initial temperature of zero: will use a Verlet 71: buffer of 10%. Check your energy drift! 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There were 2 NOTEs 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 9.00 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 71: The optimal PME mesh load for parallel simulations is below 0.5 71: and for highly parallel simulations between 0.25 and 0.33, 71: for higher performance, increase the cut-off and the PME grid spacing. 71: 71: 71: 71: There was 1 NOTE 71: Setting the LD random seed to -50486273 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -81872036 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -201918024 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: Setting the LD random seed to -492048403 71: 71: Generated 3 of the 3 non-bonded parameter combinations 71: 71: Generated 3 of the 3 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 71: 71: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: Calculating fourier grid dimensions for X Y Z 71: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 71: 71: Estimate for the relative computational load of the PME mesh part: 1.00 71: 71: This run will generate roughly 0 Mb of data 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was turned on during the run due to measured imbalance. 71: Average load imbalance: 50.7%. 71: The balanceable part of the MD step is 40%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 20.3%. 71: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 71: 71: NOTE: 20.3 % of the available CPU time was lost due to load imbalance 71: in the domain decomposition. 71: You can consider manually changing the decomposition (option -dd); 71: e.g. by using fewer domains along the box dimension in which there is 71: considerable inhomogeneity in the simulated system. 71: 71: NOTE: 21 % of the run time was spent in domain decomposition, 71: 1 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: NOTE: 16 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 7.998 2.049 390.3 71: (ns/day) (hour/ns) 71: Performance: 0.885 27.106 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (4354 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Changing nstlist from 10 to 50, rlist from 1.009 to 1.15 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: NOTE: 21 % of the run time was spent communicating energies, 71: you might want to increase some nst* mdp options 71: 71: Core t (s) Wall t (s) (%) 71: Time: 6.001 1.540 389.7 71: (ns/day) (hour/ns) 71: Performance: 1.178 20.369 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (3507 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot have separate PME ranks when PME is not used 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: 71: Dynamic load balancing report: 71: DLB was turned on during the run due to measured imbalance. 71: Average load imbalance: 27.0%. 71: The balanceable part of the MD step is 15%, load imbalance is computed from this. 71: Part of the total run time spent waiting due to load imbalance: 4.0%. 71: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 71: 71: 71: Core t (s) Wall t (s) (%) 71: Time: 10.808 2.740 394.5 71: (ns/day) (hour/ns) 71: Performance: 0.662 36.240 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (3607 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 3.589 0.917 391.4 71: (ns/day) (hour/ns) 71: Performance: 1.979 12.130 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (1264 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Changing nstlist from 10 to 100, rlist from 1 to 1 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 11.748 2.992 392.7 71: (ns/day) (hour/ns) 71: Performance: 0.606 39.576 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (3463 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 71: Changing nstlist from 10 to 100, rlist from 1 to 1 71: 71: Using 2 MPI threads 71: Using 2 OpenMP threads per tMPI thread 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 20 steps, 0.0 ps. 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 2.867 0.741 387.0 71: (ns/day) (hour/ns) 71: Performance: 2.449 9.799 71: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (1055 ms) 71: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: ./src/programs/mdrun/tests/domain_decomposition.cpp:372: Skipped 71: Test configuration is invalid: 71: Cannot use two separate PME ranks when there are only two ranks total 71: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 71: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (17254 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 16 tests from 2 test suites ran. (24544 ms total) 71: [ PASSED ] 10 tests. 71: [ SKIPPED ] 6 tests, listed below: 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 71: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 71/87 Test #71: MdrunMpiTests ............................. Passed 24.59 sec test 72 Start 72: MdrunMultiSimTests 72: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-multisim-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMultiSimTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 2 tests from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from InNvt/MultiSimTerminationTest 72: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 72: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 72: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 72: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (0 ms) 72: [----------] 2 tests from InNvt/MultiSimTerminationTest (20 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 2 tests from 1 test suite ran. (69 ms total) 72: [ PASSED ] 2 tests. 72: 72: YOU HAVE 4 DISABLED TESTS 72: 72/87 Test #72: MdrunMultiSimTests ........................ Passed 0.13 sec test 73 Start 73: MdrunMultiSimReplexTests 73: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-multisim-replex-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 1 test from 1 test suite. 73: [----------] Global test environment set-up. 73: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 73: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 73: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (0 ms) 73: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (0 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 1 test from 1 test suite ran. (37 ms total) 73: [ PASSED ] 1 test. 73: 73: YOU HAVE 4 DISABLED TESTS 73: 73/87 Test #73: MdrunMultiSimReplexTests .................. Passed 0.08 sec test 74 Start 74: MdrunMultiSimReplexEquivalenceTests 74: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-multisim-replex-equivalence-test "-ntmpi" "4" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 0 tests from 0 test suites. 74: [==========] 0 tests from 0 test suites ran. (9 ms total) 74: [ PASSED ] 0 tests. 74: 74: YOU HAVE 10 DISABLED TESTS 74: 74/87 Test #74: MdrunMultiSimReplexEquivalenceTests ....... Passed 0.06 sec test 75 Start 75: MdrunMpi1RankPmeTests 75: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 19 tests from 1 test suite. 75: [----------] Global test environment set-up. 75: [----------] 19 tests from ReproducesEnergies/PmeTest 75: Number of degrees of freedom in T-Coupling group rest is 12.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: NVE simulation: will use the initial temperature of 1046.791 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: The optimal PME mesh load for parallel simulations is below 0.5 75: and for highly parallel simulations between 0.25 and 0.33, 75: for higher performance, increase the cut-off and the PME grid spacing. 75: 75: 75: 75: There were 2 NOTEs 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: For a correct single-point energy evaluation with nsteps = 0, use 75: continuation = yes to avoid constraining the input coordinates. 75: 75: Number of degrees of freedom in T-Coupling group rest is 13.00 75: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: NVE simulation: will use the initial temperature of 966.268 K for 75: determining the Verlet buffer size 75: 75: 75: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 75: The optimal PME mesh load for parallel simulations is below 0.5 75: and for highly parallel simulations between 0.25 and 0.33, 75: for higher performance, increase the cut-off and the PME grid spacing. 75: 75: 75: 75: There were 3 NOTEs 75: Setting the LD random seed to -1935212546 75: 75: Generated 8 of the 10 non-bonded parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'Methanol' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 75: 75: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Calculating fourier grid dimensions for X Y Z 75: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 75: 75: Estimate for the relative computational load of the PME mesh part: 1.00 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to -1077988417 75: 75: Generated 8 of the 10 non-bonded parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'Methanol' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Searching the wall atom type(s) 75: 75: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 75: 75: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: Calculating fourier grid dimensions for X Y Z 75: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 75: 75: Estimate for the relative computational load of the PME mesh part: 1.00 75: 75: This run will generate roughly 0 Mb of data 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 1.128 0.564 200.0 75: (ns/day) (hour/ns) 75: Performance: 3.217 7.459 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (608 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 1.151 0.576 200.0 75: (ns/day) (hour/ns) 75: Performance: 3.152 7.615 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (624 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 0 steps, 0.0 ps. 75: 75: NOTE: 21 % of the run time was spent in domain decomposition, 75: 13 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: Core t (s) Wall t (s) (%) 75: Time: 0.109 0.054 199.7 75: (ns/day) (hour/ns) 75: Performance: 1.587 15.118 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (131 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets using PME rank(s) but the simulation is using only one rank 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 75: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 75: Can not increase nstlist because an NVE ensemble is used 75: Using 1 MPI thread 75: Using 2 OpenMP threads 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc-and-methanol' 75: 20 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Core t (s) Wall t (s) (%) 75: Time: 1.153 0.577 200.0 75: (ns/day) (hour/ns) 75: Performance: 3.146 7.629 75: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as double precision energy file 75: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (623 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 75: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 75: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 75: Test is being skipped because: 75: it targets GPU execution, but no compatible devices were detected 75: PME GPU does not support: 75: Double-precision build of GROMACS. 75: Non-GPU build of GROMACS. 75: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 75: [----------] 19 tests from ReproducesEnergies/PmeTest (1988 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 19 tests from 1 test suite ran. (2062 ms total) 75: [ PASSED ] 4 tests. 75: [ SKIPPED ] 15 tests, listed below: 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 75: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 75/87 Test #75: MdrunMpi1RankPmeTests ..................... Passed 2.12 sec test 76 Start 76: MdrunMpi2RankPmeTests 76: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-mpi-pme-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 19 tests from 1 test suite. 76: [----------] Global test environment set-up. 76: [----------] 19 tests from ReproducesEnergies/PmeTest 76: Number of degrees of freedom in T-Coupling group rest is 12.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: NVE simulation: will use the initial temperature of 1046.791 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 2 NOTEs 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: For a correct single-point energy evaluation with nsteps = 0, use 76: continuation = yes to avoid constraining the input coordinates. 76: 76: Number of degrees of freedom in T-Coupling group rest is 13.00 76: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: NVE simulation: will use the initial temperature of 966.268 K for 76: determining the Verlet buffer size 76: 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 76: The optimal PME mesh load for parallel simulations is below 0.5 76: and for highly parallel simulations between 0.25 and 0.33, 76: for higher performance, increase the cut-off and the PME grid spacing. 76: 76: 76: 76: There were 3 NOTEs 76: Setting the LD random seed to 2122194423 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: Setting the LD random seed to 2143222590 76: 76: Generated 8 of the 10 non-bonded parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'Methanol' 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Searching the wall atom type(s) 76: 76: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 76: 76: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: Calculating fourier grid dimensions for X Y Z 76: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 76: 76: Estimate for the relative computational load of the PME mesh part: 1.00 76: 76: This run will generate roughly 0 Mb of data 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 7.3%. 76: The balanceable part of the MD step is 20%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.5%. 76: 76: 76: NOTE: 11 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 14.342 3.600 398.4 76: (ns/day) (hour/ns) 76: Performance: 0.504 47.615 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (4342 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 8.4%. 76: The balanceable part of the MD step is 22%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.9%. 76: 76: 76: NOTE: 14 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 7.728 1.956 395.1 76: (ns/day) (hour/ns) 76: Performance: 0.928 25.873 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (2731 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 0 steps, 0.0 ps. 76: 76: NOTE: 18 % of the run time was spent in domain decomposition, 76: 1 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.562 0.184 304.8 76: (ns/day) (hour/ns) 76: Performance: 0.469 51.191 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (615 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 3.188 0.797 400.0 76: (ns/day) (hour/ns) 76: Performance: 2.277 10.542 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (1604 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Core t (s) Wall t (s) (%) 76: Time: 3.760 0.986 381.4 76: (ns/day) (hour/ns) 76: Performance: 1.840 13.042 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (1251 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 0 steps, 0.0 ps. 76: 76: NOTE: 14 % of the run time was spent in domain decomposition, 76: 2 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Core t (s) Wall t (s) (%) 76: Time: 0.315 0.126 250.6 76: (ns/day) (hour/ns) 76: Performance: 0.688 34.888 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (1031 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 76: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 76: Can not increase nstlist because an NVE ensemble is used 76: Using 2 MPI threads 76: Using 2 OpenMP threads per tMPI thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc-and-methanol' 76: 20 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 5.8%. 76: The balanceable part of the MD step is 20%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.2%. 76: 76: 76: NOTE: 13 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: Core t (s) Wall t (s) (%) 76: Time: 12.328 3.132 393.6 76: (ns/day) (hour/ns) 76: Performance: 0.579 41.428 76: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as double precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (3808 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 76: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 76: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 76: Test is being skipped because: 76: it targets GPU execution, but no compatible devices were detected 76: it targets PME decomposition, but that is not supported 76: PME GPU does not support: 76: Double-precision build of GROMACS. 76: Non-GPU build of GROMACS. 76: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 76: [----------] 19 tests from ReproducesEnergies/PmeTest (15386 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 19 tests from 1 test suite ran. (15451 ms total) 76: [ PASSED ] 7 tests. 76: [ SKIPPED ] 12 tests, listed below: 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 76: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 76/87 Test #76: MdrunMpi2RankPmeTests ..................... Passed 15.52 sec test 77 Start 77: MdrunCoordinationBasicTests1Rank 77: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 77: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 77: Test timeout computed to be: 1920 77: [==========] Running 1 test from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 1 test from BasicPropagators/PeriodicActionsTest 77: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.015 0.015 99.7 77: (ns/day) (hour/ns) 77: Performance: 100.929 0.238 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (1) 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 96.0 77: (ns/day) (hour/ns) 77: Performance: 2238.588 0.011 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: Setting nstcalcenergy (100) equal to nstenergy (4) 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 4. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 4. 77: 77: 77: There were 5 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 95.3 77: (ns/day) (hour/ns) 77: Performance: 2696.102 0.009 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 95.5 77: (ns/day) (hour/ns) 77: Performance: 2485.112 0.010 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 95.5 77: (ns/day) (hour/ns) 77: Performance: 2501.256 0.010 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 77: that with the Verlet scheme, nstlist has no effect on the accuracy of 77: your simulation. 77: 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 77: setting nstcomm equal to nstcalcenergy for less overhead 77: 77: Number of degrees of freedom in T-Coupling group System is 33.00 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: NVE simulation: will use the initial temperature of 68.810 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 77: COM removal frequency is set to (1). 77: Other settings require a global communication frequency of 100. 77: Note that this will require additional global communication steps, 77: which will reduce performance when using multiple ranks. 77: Consider setting nstcomm to a multiple of 100. 77: 77: 77: There were 4 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI thread 77: Using 1 OpenMP thread 77: 77: 77: NOTE: Thread affinity was not set. 77: starting mdrun 'Argon' 77: 16 steps, 0.0 ps. 77: Generated 1 of the 1 non-bonded parameter combinations 77: 77: Excluding 1 bonded neighbours molecule type 'Argon' 77: 77: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 77: 77: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: 77: This run will generate roughly 0 Mb of data 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.001 0.001 95.2 77: (ns/day) (hour/ns) 77: Performance: 2541.499 0.009 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 77: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 77: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (100 ms) 77: [----------] 1 test from BasicPropagators/PeriodicActionsTest (100 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 1 test from 1 test suite ran. (128 ms total) 77: [ PASSED ] 1 test. 77/87 Test #77: MdrunCoordinationBasicTests1Rank .......... Passed 0.19 sec test 78 Start 78: MdrunCoordinationBasicTests2Ranks 78: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-basic-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 78: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 78: Test timeout computed to be: 1920 78: [==========] Running 1 test from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 1 test from BasicPropagators/PeriodicActionsTest 78: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (1) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 2.0%. 78: The balanceable part of the MD step is 53%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.1%. 78: 78: 78: NOTE: 37 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.004 0.002 195.3 78: (ns/day) (hour/ns) 78: Performance: 706.045 0.034 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (1) 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: There were 3 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 1.7%. 78: The balanceable part of the MD step is 49%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 0.8%. 78: 78: 78: NOTE: 25 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.002 0.001 190.8 78: (ns/day) (hour/ns) 78: Performance: 1593.738 0.015 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: Setting nstcalcenergy (100) equal to nstenergy (4) 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 4. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 4. 78: 78: 78: There were 5 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 2.3%. 78: The balanceable part of the MD step is 45%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.1%. 78: 78: 78: NOTE: 28 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.001 0.001 189.3 78: (ns/day) (hour/ns) 78: Performance: 1993.397 0.012 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 2.2%. 78: The balanceable part of the MD step is 45%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.0%. 78: 78: 78: NOTE: 31 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.001 0.001 189.4 78: (ns/day) (hour/ns) 78: Performance: 1861.207 0.013 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 3.2%. 78: The balanceable part of the MD step is 45%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.4%. 78: 78: 78: NOTE: 31 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.001 0.001 190.1 78: (ns/day) (hour/ns) 78: Performance: 1868.262 0.013 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 78: that with the Verlet scheme, nstlist has no effect on the accuracy of 78: your simulation. 78: 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 78: setting nstcomm equal to nstcalcenergy for less overhead 78: 78: Number of degrees of freedom in T-Coupling group System is 33.00 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: NVE simulation: will use the initial temperature of 68.810 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 78: COM removal frequency is set to (1). 78: Other settings require a global communication frequency of 100. 78: Note that this will require additional global communication steps, 78: which will reduce performance when using multiple ranks. 78: Consider setting nstcomm to a multiple of 100. 78: 78: 78: There were 4 NOTEs 78: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI threads 78: Using 1 OpenMP thread per tMPI thread 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'Argon' 78: 16 steps, 0.0 ps. 78: Generated 1 of the 1 non-bonded parameter combinations 78: 78: Excluding 1 bonded neighbours molecule type 'Argon' 78: 78: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 78: 78: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: 78: This run will generate roughly 0 Mb of data 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 2.6%. 78: The balanceable part of the MD step is 44%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.2%. 78: 78: 78: NOTE: 31 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.002 0.001 189.3 78: (ns/day) (hour/ns) 78: Performance: 1798.188 0.013 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 78: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 78: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2457 ms) 78: [----------] 1 test from BasicPropagators/PeriodicActionsTest (2458 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 1 test from 1 test suite ran. (2482 ms total) 78: [ PASSED ] 1 test. 78/87 Test #78: MdrunCoordinationBasicTests2Ranks ......... Passed 2.53 sec test 79 Start 79: MdrunCoordinationCouplingTests1Rank 79: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 79: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 79: Test timeout computed to be: 1920 79: [==========] Running 25 tests from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.002 0.002 97.9 79: (ns/day) (hour/ns) 79: Performance: 848.099 0.028 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.1 79: (ns/day) (hour/ns) 79: Performance: 2319.501 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 2592.842 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2475.128 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.6 79: (ns/day) (hour/ns) 79: Performance: 112.644 0.213 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.6 79: (ns/day) (hour/ns) 79: Performance: 2396.186 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (105 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 1865.151 0.013 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2046.029 0.012 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.9 79: (ns/day) (hour/ns) 79: Performance: 2452.466 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2373.110 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 2510.429 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.009 99.4 79: (ns/day) (hour/ns) 79: Performance: 165.155 0.145 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (91 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 1830.786 0.013 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2254.976 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.005 0.005 98.8 79: (ns/day) (hour/ns) 79: Performance: 303.507 0.079 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2250.034 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2276.642 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.005 0.005 99.2 79: (ns/day) (hour/ns) 79: Performance: 300.502 0.080 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (48 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 1732.938 0.014 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.004 0.004 99.0 79: (ns/day) (hour/ns) 79: Performance: 401.708 0.060 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2631.608 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2427.342 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2466.210 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2309.934 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (41 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 2006.055 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2208.890 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2491.142 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2441.773 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2330.909 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2524.833 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (32 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 1900.831 0.013 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2144.307 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 2536.267 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2497.201 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.4 79: (ns/day) (hour/ns) 79: Performance: 2211.268 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2266.591 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (42 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 1957.608 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2216.041 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.005 0.005 99.1 79: (ns/day) (hour/ns) 79: Performance: 299.829 0.080 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.3 79: (ns/day) (hour/ns) 79: Performance: 2182.286 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2378.608 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2306.475 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (64 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.1 79: (ns/day) (hour/ns) 79: Performance: 1960.724 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 85 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.005 0.005 99.2 79: (ns/day) (hour/ns) 79: Performance: 301.591 0.080 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2369.459 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 90.6 79: (ns/day) (hour/ns) 79: Performance: 2258.282 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 2479.112 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.9 79: (ns/day) (hour/ns) 79: Performance: 2438.873 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (62 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 1960.724 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2322.124 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2475.128 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2434.055 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2585.226 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2595.027 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (99 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 1841.732 0.013 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2368.548 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.5 79: (ns/day) (hour/ns) 79: Performance: 2761.360 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2514.528 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2366.728 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2467.198 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (109 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 1950.790 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.029 0.029 99.8 79: (ns/day) (hour/ns) 79: Performance: 50.896 0.472 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2536.267 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.3 79: (ns/day) (hour/ns) 79: Performance: 2267.425 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.8 79: (ns/day) (hour/ns) 79: Performance: 2374.940 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.4 79: (ns/day) (hour/ns) 79: Performance: 2317.755 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (144 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.3 79: (ns/day) (hour/ns) 79: Performance: 2012.608 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2340.651 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 87.530 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.5 79: (ns/day) (hour/ns) 79: Performance: 2388.753 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.6 79: (ns/day) (hour/ns) 79: Performance: 2228.869 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 79: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 79: 1 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.5 79: (ns/day) (hour/ns) 79: Performance: 2367.638 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (131 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.5 79: (ns/day) (hour/ns) 79: Performance: 1977.084 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 2030.519 0.012 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 2345.999 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2245.114 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 2386.902 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.009 99.6 79: (ns/day) (hour/ns) 79: Performance: 165.163 0.145 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (122 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.4 79: (ns/day) (hour/ns) 79: Performance: 1753.656 0.014 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2189.266 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 2532.098 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2325.630 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.9 79: (ns/day) (hour/ns) 79: Performance: 2345.999 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.8 79: (ns/day) (hour/ns) 79: Performance: 86.973 0.276 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (128 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 1875.942 0.013 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 2193.163 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2324.752 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.5 79: (ns/day) (hour/ns) 79: Performance: 113.265 0.212 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.9 79: (ns/day) (hour/ns) 79: Performance: 2238.588 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.4 79: (ns/day) (hour/ns) 79: Performance: 2133.170 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (120 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.6 79: (ns/day) (hour/ns) 79: Performance: 1933.039 0.012 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.1 79: (ns/day) (hour/ns) 79: Performance: 2252.502 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.5 79: (ns/day) (hour/ns) 79: Performance: 2483.109 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.009 0.009 99.6 79: (ns/day) (hour/ns) 79: Performance: 165.737 0.145 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.7 79: (ns/day) (hour/ns) 79: Performance: 2158.582 0.011 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.003 0.003 98.8 79: (ns/day) (hour/ns) 79: Performance: 458.548 0.052 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (96 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.1 79: (ns/day) (hour/ns) 79: Performance: 1587.373 0.015 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.7 79: (ns/day) (hour/ns) 79: Performance: 1716.043 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.5 79: (ns/day) (hour/ns) 79: Performance: 1982.811 0.012 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.1 79: (ns/day) (hour/ns) 79: Performance: 1720.836 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 86.568 0.277 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.7 79: (ns/day) (hour/ns) 79: Performance: 1551.396 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (125 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.021 0.021 99.8 79: (ns/day) (hour/ns) 79: Performance: 69.046 0.348 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.7 79: (ns/day) (hour/ns) 79: Performance: 1641.075 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.019 4.2 79: (ns/day) (hour/ns) 79: Performance: 76.628 0.313 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.0 79: (ns/day) (hour/ns) 79: Performance: 1675.896 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.5 79: (ns/day) (hour/ns) 79: Performance: 1687.834 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.8 79: (ns/day) (hour/ns) 79: Performance: 1724.208 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (130 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 97.0 79: (ns/day) (hour/ns) 79: Performance: 1490.226 0.016 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.6 79: (ns/day) (hour/ns) 79: Performance: 1625.486 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.010 0.010 99.6 79: (ns/day) (hour/ns) 79: Performance: 145.455 0.165 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.9 79: (ns/day) (hour/ns) 79: Performance: 1675.896 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.011 0.011 99.7 79: (ns/day) (hour/ns) 79: Performance: 132.803 0.181 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.2 79: (ns/day) (hour/ns) 79: Performance: 1481.268 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (127 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.003 0.003 98.1 79: (ns/day) (hour/ns) 79: Performance: 493.914 0.049 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.9 79: (ns/day) (hour/ns) 79: Performance: 1656.964 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 87.729 0.274 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 1633.243 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.004 0.004 98.5 79: (ns/day) (hour/ns) 79: Performance: 381.154 0.063 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.5 79: (ns/day) (hour/ns) 79: Performance: 112.440 0.213 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (122 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 1345.695 0.018 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.1 79: (ns/day) (hour/ns) 79: Performance: 1475.238 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.5 79: (ns/day) (hour/ns) 79: Performance: 1688.759 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.6 79: (ns/day) (hour/ns) 79: Performance: 1620.356 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.038 0.038 99.9 79: (ns/day) (hour/ns) 79: Performance: 38.281 0.627 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 79: The Berendsen barostat does not generate any strictly correct ensemble, 79: and should not be used for new production simulations (in our opinion). 79: We recommend using the C-rescale barostat instead. 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: 79: There was 1 WARNING 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.9 79: (ns/day) (hour/ns) 79: Performance: 1653.407 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (210 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.7 79: (ns/day) (hour/ns) 79: Performance: 58.170 0.413 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 1429.704 0.017 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.008 0.008 99.1 79: (ns/day) (hour/ns) 79: Performance: 178.304 0.135 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 1615.258 0.015 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.8 79: (ns/day) (hour/ns) 79: Performance: 1721.317 0.014 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.025 0.025 99.8 79: (ns/day) (hour/ns) 79: Performance: 58.393 0.411 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (202 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.3 79: (ns/day) (hour/ns) 79: Performance: 1255.470 0.019 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 1455.029 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.7 79: (ns/day) (hour/ns) 79: Performance: 85.411 0.281 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.5 79: (ns/day) (hour/ns) 79: Performance: 1388.459 0.017 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.9 79: (ns/day) (hour/ns) 79: Performance: 1485.913 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.5 79: (ns/day) (hour/ns) 79: Performance: 1454.342 0.017 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (170 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: NOTE: 91 % of the run time was spent in pair search, 79: you might want to increase nstlist (this has no effect on accuracy) 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.018 0.018 99.7 79: (ns/day) (hour/ns) 79: Performance: 83.269 0.288 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 3 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.1 79: (ns/day) (hour/ns) 79: Performance: 1161.500 0.021 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.017 0.017 99.6 79: (ns/day) (hour/ns) 79: Performance: 84.289 0.285 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 1150.008 0.021 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.1 79: (ns/day) (hour/ns) 79: Performance: 1192.296 0.020 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: for current Trotter decomposition methods with vv, nsttcouple and 79: nstpcouple must be equal. Both have been reset to 79: min(nsttcouple,nstpcouple) = 2 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 79: COM removal frequency is set to (5). 79: Other settings require a global communication frequency of 2. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 2. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.014 0.014 99.5 79: (ns/day) (hour/ns) 79: Performance: 107.738 0.223 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (136 ms) 79: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.8 79: (ns/day) (hour/ns) 79: Performance: 1240.305 0.019 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.013 0.013 99.6 79: (ns/day) (hour/ns) 79: Performance: 110.516 0.217 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.5 79: (ns/day) (hour/ns) 79: Performance: 1452.970 0.017 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.005 0.005 99.0 79: (ns/day) (hour/ns) 79: Performance: 282.985 0.085 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.5 79: (ns/day) (hour/ns) 79: Performance: 1344.521 0.018 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: There were 2 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 79: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 79: 79: Using 1 MPI thread 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 96.0 79: (ns/day) (hour/ns) 79: Performance: 1461.588 0.016 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 79: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (66 ms) 79: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (2736 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 25 tests from 1 test suite ran. (2764 ms total) 79: [ PASSED ] 25 tests. 79/87 Test #79: MdrunCoordinationCouplingTests1Rank ....... Passed 2.82 sec test 80 Start 80: MdrunCoordinationCouplingTests2Ranks 80: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-coupling-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 80: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 25 tests from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.7%. 80: The balanceable part of the MD step is 0%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.0%. 80: 80: 80: NOTE: 35 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.468 0.234 199.9 80: (ns/day) (hour/ns) 80: Performance: 6.279 3.822 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.6%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.3 80: (ns/day) (hour/ns) 80: Performance: 1801.607 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.9%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.5%. 80: 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.2 80: (ns/day) (hour/ns) 80: Performance: 2024.846 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.2%. 80: The balanceable part of the MD step is 38%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.7 80: (ns/day) (hour/ns) 80: Performance: 1807.421 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.7%. 80: The balanceable part of the MD step is 34%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.4 80: (ns/day) (hour/ns) 80: Performance: 1822.931 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 72.3%. 80: The balanceable part of the MD step is 16%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 11.6%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 11.6 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 26 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 13 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.546 0.273 200.0 80: (ns/day) (hour/ns) 80: Performance: 5.383 4.458 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (2457 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 15.0%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 7.6%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 7.6 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 14 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 41 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.029 1.562 193.9 80: (ns/day) (hour/ns) 80: Performance: 0.940 25.523 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 20.1%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 10.2%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 10.2 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 60 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.459 1.258 195.4 80: (ns/day) (hour/ns) 80: Performance: 1.167 20.557 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.4%. 80: The balanceable part of the MD step is 40%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.6%. 80: 80: 80: NOTE: 90 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.127 0.127 99.6 80: (ns/day) (hour/ns) 80: Performance: 11.528 2.082 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.8%. 80: The balanceable part of the MD step is 0%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.0%. 80: 80: 80: NOTE: 61 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.302 0.151 199.9 80: (ns/day) (hour/ns) 80: Performance: 9.734 2.466 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.4%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.3 80: (ns/day) (hour/ns) 80: Performance: 1692.006 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.6%. 80: The balanceable part of the MD step is 21%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.3%. 80: 80: 80: NOTE: 33 % of the run time was spent in domain decomposition, 80: 3 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 23 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 192.4 80: (ns/day) (hour/ns) 80: Performance: 1275.749 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (11090 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.6%. 80: The balanceable part of the MD step is 49%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 25 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.9 80: (ns/day) (hour/ns) 80: Performance: 1344.961 0.018 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.2 80: (ns/day) (hour/ns) 80: Performance: 1740.281 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.0%. 80: The balanceable part of the MD step is 44%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.1 80: (ns/day) (hour/ns) 80: Performance: 1932.129 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.0%. 80: The balanceable part of the MD step is 42%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.4 80: (ns/day) (hour/ns) 80: Performance: 1745.953 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.2%. 80: The balanceable part of the MD step is 46%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.2 80: (ns/day) (hour/ns) 80: Performance: 1702.998 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 16.3%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 8.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 8.1 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 44 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.816 1.442 195.3 80: (ns/day) (hour/ns) 80: Performance: 1.019 23.561 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (6255 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 25 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 192.0 80: (ns/day) (hour/ns) 80: Performance: 1447.508 0.017 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 21.4%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 11.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 11.1 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 18 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.907 1.502 193.6 80: (ns/day) (hour/ns) 80: Performance: 0.978 24.536 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.1%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.0 80: (ns/day) (hour/ns) 80: Performance: 1798.451 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.1%. 80: The balanceable part of the MD step is 41%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.3 80: (ns/day) (hour/ns) 80: Performance: 1750.666 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 19.3%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 9.7%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 9.7 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 15 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 45 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.352 1.720 194.9 80: (ns/day) (hour/ns) 80: Performance: 0.854 28.104 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 7.9%. 80: The balanceable part of the MD step is 39%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 3.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.4 80: (ns/day) (hour/ns) 80: Performance: 1561.819 0.015 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (9843 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.7 80: (ns/day) (hour/ns) 80: Performance: 1529.442 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.8 80: (ns/day) (hour/ns) 80: Performance: 1883.398 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.6 80: (ns/day) (hour/ns) 80: Performance: 2308.203 0.010 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.2 80: (ns/day) (hour/ns) 80: Performance: 1924.584 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 43 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.872 0.970 193.0 80: (ns/day) (hour/ns) 80: Performance: 1.514 15.849 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 43 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.652 0.850 194.3 80: (ns/day) (hour/ns) 80: Performance: 1.728 13.889 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (6256 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 46 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.028 1.040 195.0 80: (ns/day) (hour/ns) 80: Performance: 1.412 16.993 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.564 0.818 191.2 80: (ns/day) (hour/ns) 80: Performance: 1.796 13.364 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 60 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.964 1.018 192.9 80: (ns/day) (hour/ns) 80: Performance: 1.443 16.634 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.4 80: (ns/day) (hour/ns) 80: Performance: 1835.422 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 11 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 48 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.258 0.629 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.335 10.277 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.1 80: (ns/day) (hour/ns) 80: Performance: 2021.524 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (9036 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 26 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.0 80: (ns/day) (hour/ns) 80: Performance: 1428.709 0.017 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.0 80: (ns/day) (hour/ns) 80: Performance: 1800.027 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 4.912 2.538 193.5 80: (ns/day) (hour/ns) 80: Performance: 0.579 41.472 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent in domain decomposition, 80: 2 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 17 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 193.7 80: (ns/day) (hour/ns) 80: Performance: 960.192 0.025 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 1858.680 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.1 80: (ns/day) (hour/ns) 80: Performance: 1904.945 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (10735 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.4 80: (ns/day) (hour/ns) 80: Performance: 1538.418 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.360 1.228 192.2 80: (ns/day) (hour/ns) 80: Performance: 1.196 20.065 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 2194.334 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.968 2.040 194.5 80: (ns/day) (hour/ns) 80: Performance: 0.720 33.333 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.564 1.842 193.5 80: (ns/day) (hour/ns) 80: Performance: 0.797 30.098 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.7 80: (ns/day) (hour/ns) 80: Performance: 2032.528 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (12502 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 4.756 2.440 194.9 80: (ns/day) (hour/ns) 80: Performance: 0.602 39.869 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.8 80: (ns/day) (hour/ns) 80: Performance: 1965.102 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.6 80: (ns/day) (hour/ns) 80: Performance: 2246.752 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 44 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.540 1.313 193.5 80: (ns/day) (hour/ns) 80: Performance: 1.119 21.448 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.7 80: (ns/day) (hour/ns) 80: Performance: 1869.679 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 41 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.000 1.044 191.5 80: (ns/day) (hour/ns) 80: Performance: 1.407 17.059 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (12585 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 47 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.704 1.388 194.8 80: (ns/day) (hour/ns) 80: Performance: 1.058 22.679 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 67 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.138 0.069 199.9 80: (ns/day) (hour/ns) 80: Performance: 21.262 1.129 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.4 80: (ns/day) (hour/ns) 80: Performance: 2150.670 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 55 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.104 1.604 193.5 80: (ns/day) (hour/ns) 80: Performance: 0.916 26.209 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.2 80: (ns/day) (hour/ns) 80: Performance: 1936.989 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.7 80: (ns/day) (hour/ns) 80: Performance: 1782.837 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (10071 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.4 80: (ns/day) (hour/ns) 80: Performance: 1501.485 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 57 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.584 1.340 192.8 80: (ns/day) (hour/ns) 80: Performance: 1.096 21.895 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 26 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 47 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.869 0.435 200.0 80: (ns/day) (hour/ns) 80: Performance: 3.379 7.102 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.1 80: (ns/day) (hour/ns) 80: Performance: 1947.090 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.6 80: (ns/day) (hour/ns) 80: Performance: 1939.734 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.468 1.280 192.8 80: (ns/day) (hour/ns) 80: Performance: 1.148 20.914 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (8251 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.4 80: (ns/day) (hour/ns) 80: Performance: 1490.226 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.4 80: (ns/day) (hour/ns) 80: Performance: 1797.664 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.8 80: (ns/day) (hour/ns) 80: Performance: 2091.172 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 2022.851 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.6 80: (ns/day) (hour/ns) 80: Performance: 1989.535 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 80: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 80: 1 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.8 80: (ns/day) (hour/ns) 80: Performance: 2006.381 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1967 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 192.4 80: (ns/day) (hour/ns) 80: Performance: 1528.873 0.016 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 22 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.977 0.489 200.0 80: (ns/day) (hour/ns) 80: Performance: 3.005 7.986 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.9 80: (ns/day) (hour/ns) 80: Performance: 2220.834 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 17 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 16 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.413 0.707 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.078 11.547 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 1971.705 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.7 80: (ns/day) (hour/ns) 80: Performance: 1978.989 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (9779 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 29 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.3 80: (ns/day) (hour/ns) 80: Performance: 1579.639 0.015 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.5 80: (ns/day) (hour/ns) 80: Performance: 1697.835 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.5 80: (ns/day) (hour/ns) 80: Performance: 2129.851 0.011 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 20 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 38 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.425 0.713 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.061 11.645 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.979 0.990 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.484 16.171 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 35 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 186.1 80: (ns/day) (hour/ns) 80: Performance: 1697.601 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (6555 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 43 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.545 1.273 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.154 20.796 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 58 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.006 0.003 197.6 80: (ns/day) (hour/ns) 80: Performance: 478.679 0.050 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 59 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.920 1.514 192.9 80: (ns/day) (hour/ns) 80: Performance: 0.970 24.738 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 46 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.330 0.165 199.9 80: (ns/day) (hour/ns) 80: Performance: 8.912 2.693 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.224 1.668 193.3 80: (ns/day) (hour/ns) 80: Performance: 0.881 27.255 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 189.5 80: (ns/day) (hour/ns) 80: Performance: 2008.016 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (14151 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 192.2 80: (ns/day) (hour/ns) 80: Performance: 1592.914 0.015 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 28 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 191.0 80: (ns/day) (hour/ns) 80: Performance: 1869.679 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 190.4 80: (ns/day) (hour/ns) 80: Performance: 2015.242 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 1977.401 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 35 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 190.2 80: (ns/day) (hour/ns) 80: Performance: 1961.973 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 32 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 190.2 80: (ns/day) (hour/ns) 80: Performance: 1926.992 0.012 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (619 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.6%. 80: The balanceable part of the MD step is 60%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 191.2 80: (ns/day) (hour/ns) 80: Performance: 1092.498 0.022 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.1%. 80: The balanceable part of the MD step is 57%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.7 80: (ns/day) (hour/ns) 80: Performance: 1206.304 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.4%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.7%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 1386.272 0.017 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.9%. 80: The balanceable part of the MD step is 46%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.8%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.1 80: (ns/day) (hour/ns) 80: Performance: 1359.654 0.018 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 35.1%. 80: The balanceable part of the MD step is 43%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 15.1%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 15.1 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 12 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 17 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.929 1.465 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.003 23.934 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.5%. 80: The balanceable part of the MD step is 42%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.5%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.4 80: (ns/day) (hour/ns) 80: Performance: 1303.002 0.018 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (4743 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.5%. 80: The balanceable part of the MD step is 58%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 191.5 80: (ns/day) (hour/ns) 80: Performance: 934.698 0.026 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.6%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.658 0.829 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.772 13.548 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.3%. 80: The balanceable part of the MD step is 53%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 1281.588 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.1%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.1%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.2 80: (ns/day) (hour/ns) 80: Performance: 1219.316 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.7%. 80: The balanceable part of the MD step is 52%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.0 80: (ns/day) (hour/ns) 80: Performance: 1240.180 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 10.2%. 80: The balanceable part of the MD step is 64%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 6.5%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 6.5 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 47 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 7.416 3.756 197.5 80: (ns/day) (hour/ns) 80: Performance: 0.391 61.369 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (8384 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.3%. 80: The balanceable part of the MD step is 59%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 191.4 80: (ns/day) (hour/ns) 80: Performance: 1048.612 0.023 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 11.3%. 80: The balanceable part of the MD step is 64%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 7.2%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 7.2 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 52 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 4.510 2.255 200.0 80: (ns/day) (hour/ns) 80: Performance: 0.651 36.845 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 11.9%. 80: The balanceable part of the MD step is 67%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 8.0%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 8.0 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 53 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 6.631 3.365 197.0 80: (ns/day) (hour/ns) 80: Performance: 0.436 54.990 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 5.7%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 2.9%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.5 80: (ns/day) (hour/ns) 80: Performance: 1187.813 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was turned on during the run due to measured imbalance. 80: Average load imbalance: 11.0%. 80: The balanceable part of the MD step is 66%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 7.2%. 80: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 80: 80: NOTE: 7.2 % of the available CPU time was lost due to load imbalance 80: in the domain decomposition. 80: You can consider manually changing the decomposition (option -dd); 80: e.g. by using fewer domains along the box dimension in which there is 80: considerable inhomogeneity in the simulated system. 80: 80: NOTE: 49 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 6.988 3.546 197.1 80: (ns/day) (hour/ns) 80: Performance: 0.414 57.938 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.9%. 80: The balanceable part of the MD step is 50%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.0%. 80: 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.131 0.065 199.8 80: (ns/day) (hour/ns) 80: Performance: 22.451 1.069 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (14375 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.830 0.415 200.0 80: (ns/day) (hour/ns) 80: Performance: 3.537 6.786 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 7 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.2 80: (ns/day) (hour/ns) 80: Performance: 1265.529 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 43 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 4.856 2.480 195.8 80: (ns/day) (hour/ns) 80: Performance: 0.592 40.521 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 44 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 4.732 2.422 195.4 80: (ns/day) (hour/ns) 80: Performance: 0.606 39.572 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 187.6 80: (ns/day) (hour/ns) 80: Performance: 1246.453 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 187.1 80: (ns/day) (hour/ns) 80: Performance: 1267.481 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (10020 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 189.0 80: (ns/day) (hour/ns) 80: Performance: 1027.965 0.023 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.5 80: (ns/day) (hour/ns) 80: Performance: 1190.913 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 186.8 80: (ns/day) (hour/ns) 80: Performance: 1280.789 0.019 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 21 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.177 1.089 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.349 17.791 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 45 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.809 1.905 200.0 80: (ns/day) (hour/ns) 80: Performance: 0.771 31.123 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 80: The Berendsen barostat does not generate any strictly correct ensemble, 80: and should not be used for new production simulations (in our opinion). 80: We recommend using the C-rescale barostat instead. 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: 80: There was 1 WARNING 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 27 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.174 1.087 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.351 17.760 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (8202 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 51 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 6.396 3.240 197.4 80: (ns/day) (hour/ns) 80: Performance: 0.453 52.937 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 57 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.744 2.914 197.1 80: (ns/day) (hour/ns) 80: Performance: 0.504 47.613 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.8 80: (ns/day) (hour/ns) 80: Performance: 1345.548 0.018 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.0 80: (ns/day) (hour/ns) 80: Performance: 1313.000 0.018 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1320.316 0.018 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 45 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.920 1.460 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.006 23.861 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (11061 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 53 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.497 2.778 197.9 80: (ns/day) (hour/ns) 80: Performance: 0.529 45.391 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 54 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 3.425 1.713 200.0 80: (ns/day) (hour/ns) 80: Performance: 0.858 27.985 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 5 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.3 80: (ns/day) (hour/ns) 80: Performance: 1132.046 0.021 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.4 80: (ns/day) (hour/ns) 80: Performance: 1120.414 0.021 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 189.0 80: (ns/day) (hour/ns) 80: Performance: 1100.204 0.022 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 190.1 80: (ns/day) (hour/ns) 80: Performance: 1203.123 0.020 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (7192 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 51 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 6.208 3.148 197.2 80: (ns/day) (hour/ns) 80: Performance: 0.467 51.435 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.002 190.0 80: (ns/day) (hour/ns) 80: Performance: 906.970 0.026 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 189.9 80: (ns/day) (hour/ns) 80: Performance: 990.449 0.024 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 10 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 6 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.370 0.685 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.143 11.198 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.024 0.012 198.7 80: (ns/day) (hour/ns) 80: Performance: 122.258 0.196 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: for current Trotter decomposition methods with vv, nsttcouple and 80: nstpcouple must be equal. Both have been reset to 80: min(nsttcouple,nstpcouple) = 2 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 80: COM removal frequency is set to (5). 80: Other settings require a global communication frequency of 2. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 2. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 10 % of the run time was spent in domain decomposition, 80: 0 % of the run time was spent in pair search, 80: you might want to increase nstlist (this has no effect on accuracy) 80: 80: NOTE: 13 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.814 0.907 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.619 14.823 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (10409 ms) 80: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 55 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 5.816 2.908 200.0 80: (ns/day) (hour/ns) 80: Performance: 0.505 47.518 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 57 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.596 0.316 188.9 80: (ns/day) (hour/ns) 80: Performance: 4.655 5.155 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 1.362 0.681 200.0 80: (ns/day) (hour/ns) 80: Performance: 2.157 11.128 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.3 80: (ns/day) (hour/ns) 80: Performance: 1130.177 0.021 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.003 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1068.435 0.022 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: There were 2 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 80: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 80: 80: Using 2 MPI threads 80: Using 1 OpenMP thread per tMPI thread 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: Writing final coordinates. 80: 80: NOTE: 21 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 2.582 1.291 200.0 80: (ns/day) (hour/ns) 80: Performance: 1.138 21.094 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as double precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as double precision energy file 80: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (8893 ms) 80: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (215444 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 25 tests from 1 test suite ran. (215492 ms total) 80: [ PASSED ] 25 tests. 80/87 Test #80: MdrunCoordinationCouplingTests2Ranks ...... Passed 215.59 sec test 81 Start 81: MdrunCoordinationConstraintsTests1Rank 81: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "1" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 81: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 13 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.3 81: (ns/day) (hour/ns) 81: Performance: 1836.790 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 2205.726 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 91.7 81: (ns/day) (hour/ns) 81: Performance: 2373.110 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2210.475 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2352.269 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.7 81: (ns/day) (hour/ns) 81: Performance: 114.176 0.210 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (7602 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1755.655 0.014 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2108.348 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2371.283 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2156.316 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.7 81: (ns/day) (hour/ns) 81: Performance: 2150.294 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2073.576 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (7321 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 1743.235 0.014 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2098.295 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2415.919 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.1 81: (ns/day) (hour/ns) 81: Performance: 2116.315 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.1 81: (ns/day) (hour/ns) 81: Performance: 2078.473 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.9 81: (ns/day) (hour/ns) 81: Performance: 2291.888 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (7278 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 1848.363 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 2052.163 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.5 81: (ns/day) (hour/ns) 81: Performance: 2394.323 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.7 81: (ns/day) (hour/ns) 81: Performance: 114.518 0.210 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2353.168 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.7 81: (ns/day) (hour/ns) 81: Performance: 2296.159 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6594 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 1665.475 0.014 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 2091.882 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2341.541 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.8 81: (ns/day) (hour/ns) 81: Performance: 87.088 0.276 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2320.374 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.1 81: (ns/day) (hour/ns) 81: Performance: 2151.797 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (6088 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.2 81: (ns/day) (hour/ns) 81: Performance: 1788.271 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 2179.198 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.9 81: (ns/day) (hour/ns) 81: Performance: 2466.210 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.7 81: (ns/day) (hour/ns) 81: Performance: 2152.548 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2333.558 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.7 81: (ns/day) (hour/ns) 81: Performance: 86.895 0.276 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (6862 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.5 81: (ns/day) (hour/ns) 81: Performance: 1677.265 0.014 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1993.720 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 2139.838 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.075 0.342 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.152 0.342 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.7 81: (ns/day) (hour/ns) 81: Performance: 86.831 0.276 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (8687 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.7 81: (ns/day) (hour/ns) 81: Performance: 1698.537 0.014 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.8 81: (ns/day) (hour/ns) 81: Performance: 1886.859 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 2106.186 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 70.130 0.342 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.1 81: (ns/day) (hour/ns) 81: Performance: 1995.011 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.025 0.025 99.8 81: (ns/day) (hour/ns) 81: Performance: 58.796 0.408 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (7364 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.5 81: (ns/day) (hour/ns) 81: Performance: 1691.541 0.014 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.3 81: (ns/day) (hour/ns) 81: Performance: 1774.365 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1990.499 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.3 81: (ns/day) (hour/ns) 81: Performance: 1491.669 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 1813.006 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.009 0.009 99.6 81: (ns/day) (hour/ns) 81: Performance: 159.535 0.150 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (5880 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.5 81: (ns/day) (hour/ns) 81: Performance: 1326.285 0.018 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1455.717 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.8 81: (ns/day) (hour/ns) 81: Performance: 1680.467 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.2 81: (ns/day) (hour/ns) 81: Performance: 1604.321 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1511.061 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 5 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.1 81: (ns/day) (hour/ns) 81: Performance: 1662.330 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (5934 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.029 0.029 99.9 81: (ns/day) (hour/ns) 81: Performance: 49.909 0.481 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1343.641 0.018 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.021 0.021 99.8 81: (ns/day) (hour/ns) 81: Performance: 69.311 0.346 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.2 81: (ns/day) (hour/ns) 81: Performance: 1486.630 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.3 81: (ns/day) (hour/ns) 81: Performance: 1480.912 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: NVE simulation: will use the initial temperature of 398.997 K for 81: determining the Verlet buffer size 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1530.963 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (8268 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.8 81: (ns/day) (hour/ns) 81: Performance: 1282.388 0.019 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1467.507 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.9 81: (ns/day) (hour/ns) 81: Performance: 1498.563 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.2 81: (ns/day) (hour/ns) 81: Performance: 1518.884 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 1430.700 0.017 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.4 81: (ns/day) (hour/ns) 81: Performance: 1573.989 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (7096 ms) 81: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.7 81: (ns/day) (hour/ns) 81: Performance: 84.231 0.285 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.2 81: (ns/day) (hour/ns) 81: Performance: 1375.747 0.017 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.8 81: (ns/day) (hour/ns) 81: Performance: 1535.542 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.2 81: (ns/day) (hour/ns) 81: Performance: 1452.628 0.017 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1441.075 0.017 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generating 1-4 interactions: fudge = 0.5 81: Number of degrees of freedom in T-Coupling group System is 27.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: You are using a plain Coulomb cut-off, which might produce artifacts. 81: You might want to consider using PME electrostatics. 81: 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 81: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 81: 81: Using 1 MPI thread 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'spc2' 81: 16 steps, 0.0 ps. 81: Generated 330891 of the 330891 non-bonded parameter combinations 81: 81: Generated 330891 of the 330891 1-4 parameter combinations 81: 81: Excluding 2 bonded neighbours molecule type 'SOL' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.013 0.013 99.4 81: (ns/day) (hour/ns) 81: Performance: 112.145 0.214 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 81: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (7624 ms) 81: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (92602 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 13 tests from 1 test suite ran. (92622 ms total) 81: [ PASSED ] 13 tests. 81/87 Test #81: MdrunCoordinationConstraintsTests1Rank .... Passed 92.67 sec test 82 Start 82: MdrunCoordinationConstraintsTests2Ranks 82: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-coordination-constraints-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 82: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 13 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 53%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 192.0 82: (ns/day) (hour/ns) 82: Performance: 1357.557 0.018 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 41%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 13 % of the run time was spent in domain decomposition, 82: 4 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 24 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.7 82: (ns/day) (hour/ns) 82: Performance: 1412.009 0.017 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.8%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: NOTE: 26 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 1907.009 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.7%. 82: The balanceable part of the MD step is 38%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 28 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 1832.965 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.0%. 82: The balanceable part of the MD step is 38%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.2%. 82: 82: 82: NOTE: 28 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 189.4 82: (ns/day) (hour/ns) 82: Performance: 1872.236 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.5%. 82: The balanceable part of the MD step is 38%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 28 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1830.786 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (9869 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 53%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 24 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 192.1 82: (ns/day) (hour/ns) 82: Performance: 1299.155 0.018 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.8%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.1 82: (ns/day) (hour/ns) 82: Performance: 1571.781 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.1%. 82: The balanceable part of the MD step is 43%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 27 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.3 82: (ns/day) (hour/ns) 82: Performance: 1861.207 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 43%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.5 82: (ns/day) (hour/ns) 82: Performance: 1712.941 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 43%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.5 82: (ns/day) (hour/ns) 82: Performance: 1682.763 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.6%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.7 82: (ns/day) (hour/ns) 82: Performance: 1741.511 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (9516 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 54%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.2 82: (ns/day) (hour/ns) 82: Performance: 1325.857 0.018 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.9%. 82: The balanceable part of the MD step is 49%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.7 82: (ns/day) (hour/ns) 82: Performance: 1544.008 0.016 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 11 % of the run time was spent in domain decomposition, 82: 4 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 26 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.2 82: (ns/day) (hour/ns) 82: Performance: 1726.866 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.6 82: (ns/day) (hour/ns) 82: Performance: 1755.905 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.7 82: (ns/day) (hour/ns) 82: Performance: 1722.279 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.7%. 82: The balanceable part of the MD step is 42%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.6 82: (ns/day) (hour/ns) 82: Performance: 1850.862 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (9942 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 12 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 3.317 1.659 200.0 82: (ns/day) (hour/ns) 82: Performance: 0.886 27.103 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 5.424 2.780 195.1 82: (ns/day) (hour/ns) 82: Performance: 0.528 45.424 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 1869.963 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.0 82: (ns/day) (hour/ns) 82: Performance: 1772.833 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.3 82: (ns/day) (hour/ns) 82: Performance: 1718.676 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1731.233 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (18496 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.2 82: (ns/day) (hour/ns) 82: Performance: 1305.764 0.018 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 5.516 2.810 196.3 82: (ns/day) (hour/ns) 82: Performance: 0.523 45.914 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 5 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.7 82: (ns/day) (hour/ns) 82: Performance: 1772.578 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 6.264 3.182 196.9 82: (ns/day) (hour/ns) 82: Performance: 0.462 51.993 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1576.406 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.8 82: (ns/day) (hour/ns) 82: Performance: 1655.851 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (21000 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 3.324 1.686 197.2 82: (ns/day) (hour/ns) 82: Performance: 0.871 27.549 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.8 82: (ns/day) (hour/ns) 82: Performance: 1566.585 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.4 82: (ns/day) (hour/ns) 82: Performance: 1507.732 0.016 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.1 82: (ns/day) (hour/ns) 82: Performance: 1731.477 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.8 82: (ns/day) (hour/ns) 82: Performance: 1680.009 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 185.8 82: (ns/day) (hour/ns) 82: Performance: 1717.239 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (10683 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 192.4 82: (ns/day) (hour/ns) 82: Performance: 1288.288 0.019 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.5 82: (ns/day) (hour/ns) 82: Performance: 1516.827 0.016 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.7 82: (ns/day) (hour/ns) 82: Performance: 1658.079 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.7 82: (ns/day) (hour/ns) 82: Performance: 1669.990 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 40 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.204 0.102 199.9 82: (ns/day) (hour/ns) 82: Performance: 14.403 1.666 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 186.9 82: (ns/day) (hour/ns) 82: Performance: 1692.936 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (10560 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 15 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 23 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 5.811 2.905 200.0 82: (ns/day) (hour/ns) 82: Performance: 0.506 47.475 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 19 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.245 1.123 200.0 82: (ns/day) (hour/ns) 82: Performance: 1.308 18.344 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.0 82: (ns/day) (hour/ns) 82: Performance: 1690.149 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.5 82: (ns/day) (hour/ns) 82: Performance: 1418.511 0.017 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.0 82: (ns/day) (hour/ns) 82: Performance: 1567.182 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.9 82: (ns/day) (hour/ns) 82: Performance: 1640.419 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (21283 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 27 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 6.096 3.092 197.2 82: (ns/day) (hour/ns) 82: Performance: 0.475 50.522 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.5 82: (ns/day) (hour/ns) 82: Performance: 1500.205 0.016 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.3 82: (ns/day) (hour/ns) 82: Performance: 1578.021 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.3 82: (ns/day) (hour/ns) 82: Performance: 1613.354 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.4 82: (ns/day) (hour/ns) 82: Performance: 1668.859 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.4 82: (ns/day) (hour/ns) 82: Performance: 1531.153 0.016 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (15295 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.5%. 82: The balanceable part of the MD step is 57%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 5 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 191.3 82: (ns/day) (hour/ns) 82: Performance: 940.118 0.026 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.1%. 82: The balanceable part of the MD step is 37%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 21 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 2.105 1.053 200.0 82: (ns/day) (hour/ns) 82: Performance: 1.395 17.198 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.2 82: (ns/day) (hour/ns) 82: Performance: 1161.500 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 47%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.3 82: (ns/day) (hour/ns) 82: Performance: 1185.756 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 39%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 12 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 20 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 4.848 2.482 195.3 82: (ns/day) (hour/ns) 82: Performance: 0.592 40.552 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 5 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.6%. 82: The balanceable part of the MD step is 47%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.3 82: (ns/day) (hour/ns) 82: Performance: 1189.074 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (14564 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.5%. 82: The balanceable part of the MD step is 57%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 191.7 82: (ns/day) (hour/ns) 82: Performance: 883.113 0.027 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.9%. 82: The balanceable part of the MD step is 62%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 5 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 190.5 82: (ns/day) (hour/ns) 82: Performance: 1056.162 0.023 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 63%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 47 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 5.224 2.655 196.8 82: (ns/day) (hour/ns) 82: Performance: 0.553 43.380 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 189.6 82: (ns/day) (hour/ns) 82: Performance: 1026.509 0.023 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.3%. 82: The balanceable part of the MD step is 60%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.2%. 82: 82: 82: NOTE: 44 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 6.858 3.478 197.2 82: (ns/day) (hour/ns) 82: Performance: 0.422 56.830 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: NVE simulation: will use the initial temperature of 398.997 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.2%. 82: The balanceable part of the MD step is 61%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 45 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 7.112 3.602 197.5 82: (ns/day) (hour/ns) 82: Performance: 0.408 58.853 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (22632 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.359 0.179 199.9 82: (ns/day) (hour/ns) 82: Performance: 8.187 2.932 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.2 82: (ns/day) (hour/ns) 82: Performance: 1082.515 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.4 82: (ns/day) (hour/ns) 82: Performance: 1153.777 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.0 82: (ns/day) (hour/ns) 82: Performance: 1075.804 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.2 82: (ns/day) (hour/ns) 82: Performance: 1107.423 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.0 82: (ns/day) (hour/ns) 82: Performance: 1141.696 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (12439 ms) 82: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 8.111 4.100 197.8 82: (ns/day) (hour/ns) 82: Performance: 0.358 66.990 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.7 82: (ns/day) (hour/ns) 82: Performance: 1042.225 0.023 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 5 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.2 82: (ns/day) (hour/ns) 82: Performance: 1084.230 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.3 82: (ns/day) (hour/ns) 82: Performance: 1082.515 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1054.264 0.023 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generating 1-4 interactions: fudge = 0.5 82: Number of degrees of freedom in T-Coupling group System is 27.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: You are using a plain Coulomb cut-off, which might produce artifacts. 82: You might want to consider using PME electrostatics. 82: 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 82: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 82: 82: Using 2 MPI threads 82: Using 1 OpenMP thread per tMPI thread 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'spc2' 82: 16 steps, 0.0 ps. 82: Generated 330891 of the 330891 non-bonded parameter combinations 82: 82: Generated 330891 of the 330891 1-4 parameter combinations 82: 82: Excluding 2 bonded neighbours molecule type 'SOL' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 1024.801 0.023 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file 82: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (14964 ms) 82: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (191250 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 13 tests from 1 test suite ran. (191257 ms total) 82: [ PASSED ] 13 tests. 82/87 Test #82: MdrunCoordinationConstraintsTests2Ranks ... Passed 191.29 sec test 83 Start 83: MdrunFEPTests 83: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunFEPTests.xml" 83: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 83: Test timeout computed to be: 600 83: [==========] Running 12 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -438307841 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.93 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.786 1.393 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.303 18.425 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (double precision) 83: 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_d (1920 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -50512065 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.93 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 3.614 1.807 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.004 23.900 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_d (2499 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 4 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -335577993 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.93 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 3.592 1.796 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.010 23.758 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_d (2675 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 3 [file topol.top, line 155]: 83: System has non-zero total charge: 1.000000 83: Total charge should normally be an integer. See 83: https://manual.gromacs.org/current/user-guide/floating-point.html 83: for discussion on how close it should be to an integer. 83: 83: 83: 83: 83: WARNING 2 [file topol.top, line 155]: 83: You are using Ewald electrostatics in a system with net charge. This can 83: lead to severe artifacts, such as ions moving into regions with low 83: dielectric, due to the uniform background charge. We suggest to 83: neutralize your system with counter ions, possibly in combination with a 83: physiological salt concentration. 83: 83: Setting the LD random seed to -168036869 83: 83: Generated 171 of the 171 non-bonded parameter combinations 83: 83: Generated 171 of the 171 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'NA' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: 83: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 83: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 83: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 83: Charge 83: J. Chem. Theory Comput. 10 (2014) pp. 381-393 83: -------- -------- --- Thank You --- -------- -------- 83: 83: Number of degrees of freedom in T-Coupling group System is 358.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 5 NOTEs 83: 83: There were 2 WARNINGs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 50, rlist from 1.008 to 1.12 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: There are: 1 Ion residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 83: 83: Estimate for the relative computational load of the PME mesh part: 0.95 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.858 1.429 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.270 18.902 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_d (1651 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: NOTE 3 [file topol.top, line 165]: 83: System has non-zero total charge: 1.000000 83: Total charge should normally be an integer. See 83: https://manual.gromacs.org/current/user-guide/floating-point.html 83: for discussion on how close it should be to an integer. 83: 83: 83: 83: 83: WARNING 2 [file topol.top, line 165]: 83: You are using Ewald electrostatics in a system with net charge. This can 83: lead to severe artifacts, such as ions moving into regions with low 83: dielectric, due to the uniform background charge. We suggest to 83: neutralize your system with counter ions, possibly in combination with a 83: physiological salt concentration. 83: 83: Setting the LD random seed to -545800225 83: 83: Generated 190 of the 190 non-bonded parameter combinations 83: 83: Generated 190 of the 190 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'NA' 83: 83: turning H bonds into constraints... 83: 83: Excluding 1 bonded neighbours molecule type 'CL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'CL' 83: 83: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 83: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 83: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 83: Charge 83: J. Chem. Theory Comput. 10 (2014) pp. 381-393 83: -------- -------- --- Thank You --- -------- -------- 83: 83: Number of degrees of freedom in T-Coupling group System is 361.00 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 5 NOTEs 83: 83: There were 2 WARNINGs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 50, rlist from 1.008 to 1.121 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: There are: 2 Ion residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 83: 83: Estimate for the relative computational load of the PME mesh part: 0.95 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.341 1.171 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.550 15.484 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_d (1315 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 83: For proper sampling of the (nearly) decoupled state, stochastic dynamics 83: should be used 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 83: and vdw_modifier=Force-switch 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 4 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 100 steps, 0.1 ps. 83: Setting the LD random seed to 1810985309 83: 83: Generated 153 of the 153 non-bonded parameter combinations 83: 83: Generated 153 of the 153 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: 83: Coupling 1 copies of molecule type 'ASN' 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.93 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 13.818 6.909 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.263 19.002 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_d (7242 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: WARNING 2 [file topol.top, line 72]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 3 [file topol.top, line 73]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 4 [file topol.top, line 98]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 5 [file topol.top, line 99]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 6 [file topol.top, line 100]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 7 [file topol.top, line 101]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 8 [file topol.top, line 111]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 9 [file topol.top, line 112]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 10 [file topol.top, line 113]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 11 [file topol.top, line 114]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 2 NOTEs 83: 83: There were 11 WARNINGs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -4198568 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.93 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 4.007 2.004 200.0 83: (ns/day) (hour/ns) 83: Performance: 0.905 26.505 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_d (2477 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: 83: WARNING 2 [file topol.top, line 72]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 3 [file topol.top, line 73]: 83: No default Bond types for perturbed atoms, using normal values 83: 83: 83: WARNING 4 [file topol.top, line 98]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 5 [file topol.top, line 99]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 6 [file topol.top, line 100]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 7 [file topol.top, line 101]: 83: No default Angle types for perturbed atoms, using normal values 83: 83: 83: WARNING 8 [file topol.top, line 111]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 9 [file topol.top, line 112]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 10 [file topol.top, line 113]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: 83: WARNING 11 [file topol.top, line 114]: 83: No default Ryckaert-Bell. types for perturbed atoms, using normal values 83: 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: Removing center of mass motion in the presence of position restraints 83: might cause artifacts. When you are using position restraints to 83: equilibrate a macro-molecule, the artifacts are usually negligible. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There were 11 WARNINGs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to 2102362031 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.93 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 2.560 1.280 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.417 16.931 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_d (1737 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 2 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to 2063234414 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.87 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.727 0.864 200.0 83: (ns/day) (hour/ns) 83: Performance: 2.101 11.425 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_d (1146 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: There was 1 NOTE 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.935 0.968 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.875 12.801 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: Setting the LD random seed to -1073748003 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.87 83: 83: This run will generate roughly 0 Mb of data 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_d (1419 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to -405799461 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.93 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 3.059 1.529 200.0 83: (ns/day) (hour/ns) 83: Performance: 1.186 20.231 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_d (1951 ms) 83: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: With PME there is a minor soft core effect present at the cut-off, 83: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 83: energy conservation, but usually other effects dominate. With a common 83: sigma value of 0.34 nm the fraction of the particle-particle potential at 83: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 83: 83: 83: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: The Berendsen thermostat does not generate the correct kinetic energy 83: distribution, and should not be used for new production simulations (in 83: our opinion). We would recommend the V-rescale thermostat. 83: 83: Generating 1-4 interactions: fudge = 0.5 83: Number of degrees of freedom in T-Coupling group System is 355.00 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: The optimal PME mesh load for parallel simulations is below 0.5 83: and for highly parallel simulations between 0.25 and 0.33, 83: for higher performance, increase the cut-off and the PME grid spacing. 83: 83: 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 83: For free energy simulations, the optimal load limit increases from 0.5 to 83: 0.667 83: 83: 83: 83: There were 3 NOTEs 83: 83: There was 1 WARNING 83: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 83: Changing nstlist from 10 to 100, rlist from 1 to 1 83: 83: Using 1 MPI thread 83: Using 2 OpenMP threads 83: 83: 83: NOTE: The number of threads is not equal to the number of (logical) cpus 83: and the -pin option is set to auto: will not pin threads to cpus. 83: This can lead to significant performance degradation. 83: Consider using -pin on (and -pinoffset in case you run multiple jobs). 83: starting mdrun 'AA' 83: 20 steps, 0.0 ps. 83: Setting the LD random seed to 1064164350 83: 83: Generated 136 of the 136 non-bonded parameter combinations 83: 83: Generated 136 of the 136 1-4 parameter combinations 83: 83: Excluding 3 bonded neighbours molecule type 'ASN' 83: 83: turning H bonds into constraints... 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: 83: turning H bonds into constraints... 83: Analysing residue names: 83: There are: 1 Protein residues 83: There are: 56 Water residues 83: Analysing Protein... 83: 83: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 83: 83: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: Calculating fourier grid dimensions for X Y Z 83: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 83: 83: Estimate for the relative computational load of the PME mesh part: 0.88 83: 83: This run will generate roughly 0 Mb of data 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 1.515 0.758 200.0 83: (ns/day) (hour/ns) 83: Performance: 2.394 10.023 83: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_d_energy.edr as double precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 83: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_d (1183 ms) 83: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (27224 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 12 tests from 1 test suite ran. (27279 ms total) 83: [ PASSED ] 12 tests. 83/87 Test #83: MdrunFEPTests ............................. Passed 27.40 sec test 84 Start 84: MdrunPullTests 84: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunPullTests.xml" 84: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 84: Test timeout computed to be: 600 84: [==========] Running 4 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 4 tests from PullTest/PullIntegrationTest 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.600 nm 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.738 0.369 200.0 84: (ns/day) (hour/ns) 84: Performance: 4.916 4.882 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (1882 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.301 nm 0.400 nm 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.666 0.333 200.0 84: (ns/day) (hour/ns) 84: Performance: 5.450 4.404 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (2113 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Pull group 3 'r_3' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1292.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.357 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.500 nm 84: 1 3 2 84: 3 3 8 0.331 nm 0.400 nm 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.733 0.367 200.0 84: (ns/day) (hour/ns) 84: Performance: 4.946 4.852 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (2146 ms) 84: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 84: Generating 1-4 interactions: fudge = 0.5 84: Pull group 1 'r_1' has 3 atoms 84: Pull group 2 'r_2' has 3 atoms 84: Number of degrees of freedom in T-Coupling group System is 1293.00 84: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 84: NVE simulation: will use the initial temperature of 303.122 K for 84: determining the Verlet buffer size 84: 84: Pull group natoms pbc atom distance at start reference at t=0 84: 1 3 2 84: 2 3 5 0.575 nm 0.000 nm 84: 1 3 2 84: 2 3 5 0.050 nm 0.000 nm 84: 84: There was 1 NOTE 84: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 1 MPI thread 84: Using 2 OpenMP threads 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 20 steps, 0.0 ps. 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.736 0.368 200.0 84: (ns/day) (hour/ns) 84: Performance: 4.929 4.869 84: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as double precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (2207 ms) 84: [----------] 4 tests from PullTest/PullIntegrationTest (8369 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 4 tests from 1 test suite ran. (8417 ms total) 84: [ PASSED ] 4 tests. 84/87 Test #84: MdrunPullTests ............................ Passed 8.49 sec test 85 Start 85: MdrunRotationTests 85: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunRotationTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 12 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 12 tests from RotationWorks/RotationTest 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 85: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: trr version: GMX_trn_file (single precision) 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1076396034 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 14 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.807 0.404 200.0 85: (ns/day) (hour/ns) 85: Performance: 11.132 2.156 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (525 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 85: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1209041170 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.608 0.304 199.9 85: (ns/day) (hour/ns) 85: Performance: 14.781 1.624 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (360 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 85: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -209243473 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 16 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.615 0.308 200.0 85: (ns/day) (hour/ns) 85: Performance: 14.596 1.644 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (364 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 85: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 1769451449 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 15 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.617 0.308 200.0 85: (ns/day) (hour/ns) 85: Performance: 14.572 1.647 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (360 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 85: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -671105030 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 12 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.674 0.337 200.0 85: (ns/day) (hour/ns) 85: Performance: 13.335 1.800 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (396 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 85: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -537926163 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 13 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.733 0.367 200.0 85: (ns/day) (hour/ns) 85: Performance: 12.256 1.958 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (426 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 85: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -1410598050 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 12 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.370 0.185 199.9 85: (ns/day) (hour/ns) 85: Performance: 24.255 0.989 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (205 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 85: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 2141515263 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 11 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.411 0.206 199.9 85: (ns/day) (hour/ns) 85: Performance: 21.846 1.099 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (227 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 85: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -537410305 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 13 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.298 0.149 199.9 85: (ns/day) (hour/ns) 85: Performance: 30.186 0.795 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (187 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 85: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 938195965 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 13 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.370 0.185 199.9 85: (ns/day) (hour/ns) 85: Performance: 24.268 0.989 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (205 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 85: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to 1566305099 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 12 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.293 0.147 199.9 85: (ns/day) (hour/ns) 85: Performance: 30.623 0.784 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (166 ms) 85: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 85: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 85: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 85: that with the Verlet scheme, nstlist has no effect on the accuracy of 85: your simulation. 85: 85: Rotation group 0 'system' has 4 atoms 85: Number of degrees of freedom in T-Coupling group rest is 9.00 85: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 85: NVE simulation with an initial temperature of zero: will use a Verlet 85: buffer of 10%. Check your energy drift! 85: 85: Enforced rotation: group 0 has 4 reference positions. 85: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 85: 85: There were 2 NOTEs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 85: Can not increase nstlist because an NVE ensemble is used 85: Using 1 MPI thread 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 85: 25 steps, 0.1 ps. 85: Setting the LD random seed to -2015758338 85: 85: Generated 1 of the 1 non-bonded parameter combinations 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonA' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonB' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonC' 85: 85: Excluding 1 bonded neighbours molecule type 'ArgonD' 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: NOTE: 11 % of the run time was spent in pair search, 85: you might want to increase nstlist (this has no effect on accuracy) 85: 85: Core t (s) Wall t (s) (%) 85: Time: 0.393 0.197 200.0 85: (ns/day) (hour/ns) 85: Performance: 22.863 1.050 85: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as double precision energy file 85: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 85: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (211 ms) 85: [----------] 12 tests from RotationWorks/RotationTest (3639 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 12 tests from 1 test suite ran. (3686 ms total) 85: [ PASSED ] 12 tests. 85/87 Test #85: MdrunRotationTests ........................ Passed 3.76 sec test 86 Start 86: MdrunSimulatorComparison 86: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunSimulatorComparison.xml" 86: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 94 tests from 4 test suites. 86: [----------] Global test environment set-up. 86: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.240 0.120 199.9 86: (ns/day) (hour/ns) 86: Performance: 12.231 1.962 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.241 0.120 199.9 86: (ns/day) (hour/ns) 86: Performance: 12.209 1.966 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision) 86: 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (272 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 15 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.275 0.138 199.9 86: (ns/day) (hour/ns) 86: Performance: 10.679 2.247 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.327 0.164 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.970 2.675 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (331 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/4 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/5 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.374 0.187 200.0 86: (ns/day) (hour/ns) 86: Performance: 7.860 3.053 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.331 0.166 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.861 2.708 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/6 (412 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.309 0.155 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.503 2.526 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.327 0.164 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.971 2.675 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/7 (356 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.369 0.185 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.952 3.018 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.395 0.198 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.431 3.230 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/8 (418 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/9 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/10 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.350 0.175 200.0 86: (ns/day) (hour/ns) 86: Performance: 8.393 2.859 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.324 0.162 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.053 2.651 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/11 (383 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: 86: WARNING 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There were 2 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.238 0.119 199.9 86: (ns/day) (hour/ns) 86: Performance: 12.332 1.946 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.305 0.152 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.638 2.490 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/12 (299 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.364 0.182 200.0 86: (ns/day) (hour/ns) 86: Performance: 8.063 2.977 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.212 0.106 199.9 86: (ns/day) (hour/ns) 86: Performance: 13.830 1.735 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/13 (333 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/14 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.390 0.195 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.530 3.187 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.212 0.106 199.9 86: (ns/day) (hour/ns) 86: Performance: 13.821 1.737 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/15 (322 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.307 0.154 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.568 2.508 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.455 0.227 199.9 86: (ns/day) (hour/ns) 86: Performance: 6.456 3.717 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/16 (412 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/17 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.394 0.197 200.0 86: (ns/day) (hour/ns) 86: Performance: 7.453 3.220 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.452 0.226 199.9 86: (ns/day) (hour/ns) 86: Performance: 6.497 3.694 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/18 (478 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.575 0.287 200.0 86: (ns/day) (hour/ns) 86: Performance: 5.110 4.697 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.305 0.152 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.637 2.490 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_19_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/19 (458 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/20 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.230 0.115 199.9 86: (ns/day) (hour/ns) 86: Performance: 12.740 1.884 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.248 0.124 199.9 86: (ns/day) (hour/ns) 86: Performance: 11.820 2.030 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/21 (260 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.235 0.118 199.9 86: (ns/day) (hour/ns) 86: Performance: 12.485 1.922 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.243 0.122 199.9 86: (ns/day) (hour/ns) 86: Performance: 12.063 1.990 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/22 (259 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.237 0.119 199.9 86: (ns/day) (hour/ns) 86: Performance: 12.395 1.936 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.266 0.133 199.9 86: (ns/day) (hour/ns) 86: Performance: 11.028 2.176 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/23 (272 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/24 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/25 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: Center of mass removal not necessary for Andersen. All velocities of 86: coupled groups are rerandomized periodically, so flying ice cube errors 86: will not occur. 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.279 0.140 199.9 86: (ns/day) (hour/ns) 86: Performance: 10.517 2.282 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.295 0.147 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.971 2.407 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/26 (308 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: Center of mass removal not necessary for Andersen. All velocities of 86: coupled groups are rerandomized periodically, so flying ice cube errors 86: will not occur. 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.285 0.142 199.9 86: (ns/day) (hour/ns) 86: Performance: 10.308 2.328 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.294 0.147 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.995 2.401 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/27 (308 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: Center of mass removal not necessary for Andersen. All velocities of 86: coupled groups are rerandomized periodically, so flying ice cube errors 86: will not occur. 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.406 0.203 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.228 3.320 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.565 0.283 200.0 86: (ns/day) (hour/ns) 86: Performance: 5.196 4.619 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/28 (517 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/29 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/30 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.673 0.337 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.363 5.501 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.382 0.191 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.696 3.119 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/31 (2528 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.551 0.276 200.0 86: (ns/day) (hour/ns) 86: Performance: 5.328 4.504 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.413 0.206 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.114 3.374 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_32_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/32 (1998 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/33 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/34 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/35 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.544 0.272 200.0 86: (ns/day) (hour/ns) 86: Performance: 5.398 4.446 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.488 0.244 199.9 86: (ns/day) (hour/ns) 86: Performance: 6.015 3.990 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_36_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/36 (1937 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.568 0.284 200.0 86: (ns/day) (hour/ns) 86: Performance: 5.169 4.643 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.589 0.294 199.9 86: (ns/day) (hour/ns) 86: Performance: 4.989 4.811 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_37_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/37 (2175 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.607 0.304 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.837 4.962 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.530 0.265 199.9 86: (ns/day) (hour/ns) 86: Performance: 5.542 4.331 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_38_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/38 (2277 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/39 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/40 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.505 0.253 200.0 86: (ns/day) (hour/ns) 86: Performance: 5.813 4.129 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.634 0.317 199.9 86: (ns/day) (hour/ns) 86: Performance: 4.635 5.178 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_41_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/41 (2170 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: 86: WARNING 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There were 2 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.599 0.299 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.905 4.893 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.448 0.224 199.9 86: (ns/day) (hour/ns) 86: Performance: 6.549 3.664 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_42_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/42 (2305 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.692 0.346 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.242 5.657 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.670 0.335 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.381 5.478 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_43_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/43 (2321 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/44 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/45 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.587 0.293 200.0 86: (ns/day) (hour/ns) 86: Performance: 5.004 4.796 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.569 0.285 199.9 86: (ns/day) (hour/ns) 86: Performance: 5.163 4.649 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_46_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/46 (2361 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/47 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.641 0.320 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.583 5.236 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.642 0.321 199.9 86: (ns/day) (hour/ns) 86: Performance: 4.578 5.243 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_48_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/48 (2435 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/49 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/50 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.488 0.244 200.0 86: (ns/day) (hour/ns) 86: Performance: 6.013 3.991 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.496 0.248 199.9 86: (ns/day) (hour/ns) 86: Performance: 5.920 4.054 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_51_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/51 (2302 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.640 0.320 200.0 86: (ns/day) (hour/ns) 86: Performance: 4.588 5.231 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.775 0.388 200.0 86: (ns/day) (hour/ns) 86: Performance: 3.789 6.335 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_52_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/52 (2424 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 86: Andersen temperature control methods assume nsttcouple = 1; there is no 86: need for larger nsttcouple > 1, since no global parameters are computed. 86: nsttcouple has been reset to 1 86: 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.947 0.473 200.0 86: (ns/day) (hour/ns) 86: Performance: 3.103 7.735 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.939 0.469 200.0 86: (ns/day) (hour/ns) 86: Performance: 3.129 7.669 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_53_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/53 (3057 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/54 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/55 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/56 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/57 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/58 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 86: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/59 (0 ms) 86: [----------] 60 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (36704 ms total) 86: 86: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 13 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.247 0.124 199.9 86: (ns/day) (hour/ns) 86: Performance: 11.882 2.020 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 14 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.317 0.159 200.0 86: (ns/day) (hour/ns) 86: Performance: 9.253 2.594 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (327 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 12 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.318 0.159 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.232 2.600 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.341 0.171 200.0 86: (ns/day) (hour/ns) 86: Performance: 8.601 2.790 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (371 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 68.810 K for 86: determining the Verlet buffer size 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.328 0.164 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.951 2.681 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.345 0.173 200.0 86: (ns/day) (hour/ns) 86: Performance: 8.501 2.823 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (378 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.166 0.083 199.8 86: (ns/day) (hour/ns) 86: Performance: 17.711 1.355 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.174 0.087 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.898 1.420 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (200 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.184 0.092 199.9 86: (ns/day) (hour/ns) 86: Performance: 15.977 1.502 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.174 0.087 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.829 1.426 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (204 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.177 0.089 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.596 1.446 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.181 0.091 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.180 1.483 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (200 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.169 0.085 199.9 86: (ns/day) (hour/ns) 86: Performance: 17.350 1.383 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.215 0.107 199.9 86: (ns/day) (hour/ns) 86: Performance: 13.674 1.755 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (218 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.170 0.085 199.8 86: (ns/day) (hour/ns) 86: Performance: 17.296 1.388 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.178 0.089 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.471 1.457 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_8_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/8 (196 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.174 0.087 199.8 86: (ns/day) (hour/ns) 86: Performance: 16.901 1.420 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.171 0.086 199.9 86: (ns/day) (hour/ns) 86: Performance: 17.161 1.399 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_9_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/9 (200 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: 86: WARNING 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There were 2 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.183 0.091 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.080 1.493 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.190 0.095 199.9 86: (ns/day) (hour/ns) 86: Performance: 15.488 1.550 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_10_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/10 (205 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 2 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.173 0.086 199.9 86: (ns/day) (hour/ns) 86: Performance: 17.017 1.410 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.012 0.006 198.5 86: (ns/day) (hour/ns) 86: Performance: 248.983 0.096 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_11_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/11 (117 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.174 0.087 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.902 1.420 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.169 0.085 199.9 86: (ns/day) (hour/ns) 86: Performance: 17.334 1.385 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_12_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/12 (194 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.169 0.085 199.8 86: (ns/day) (hour/ns) 86: Performance: 17.326 1.385 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.177 0.088 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.599 1.446 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_13_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/13 (191 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.209 0.104 199.9 86: (ns/day) (hour/ns) 86: Performance: 14.064 1.707 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.256 0.128 199.9 86: (ns/day) (hour/ns) 86: Performance: 11.450 2.096 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_14_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/14 (259 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Number of degrees of freedom in T-Coupling group System is 33.00 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: Generated 1 of the 1 non-bonded parameter combinations 86: 86: Excluding 1 bonded neighbours molecule type 'Argon' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.215 0.107 199.9 86: (ns/day) (hour/ns) 86: Performance: 13.665 1.756 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 100, rlist from 0.703 to 0.752 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'Argon' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.178 0.089 199.9 86: (ns/day) (hour/ns) 86: Performance: 16.456 1.458 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_15_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/15 (234 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.133 0.067 199.8 86: (ns/day) (hour/ns) 86: Performance: 22.056 1.088 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.218 0.109 199.9 86: (ns/day) (hour/ns) 86: Performance: 13.469 1.782 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_16_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/16 (666 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.456 0.228 199.9 86: (ns/day) (hour/ns) 86: Performance: 6.439 3.727 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.447 0.224 200.0 86: (ns/day) (hour/ns) 86: Performance: 6.571 3.652 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_17_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/17 (2019 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: NVE simulation: will use the initial temperature of 398.997 K for 86: determining the Verlet buffer size 86: 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 10 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.306 0.153 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.591 2.502 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.354 0.177 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.288 2.896 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_18_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/18 (1954 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/19 (0 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.451 0.226 199.9 86: (ns/day) (hour/ns) 86: Performance: 6.512 3.686 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.056 0.028 199.6 86: (ns/day) (hour/ns) 86: Performance: 52.308 0.459 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_20_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/20 (1793 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.359 0.180 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.180 2.934 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.379 0.189 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.757 3.094 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_21_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/21 (1836 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.393 0.197 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.474 3.211 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.405 0.203 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.243 3.314 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_22_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/22 (1674 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.316 0.158 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.295 2.582 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.333 0.166 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.823 2.720 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_23_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/23 (1988 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.398 0.199 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.370 3.256 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.382 0.191 200.0 86: (ns/day) (hour/ns) 86: Performance: 7.679 3.126 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_24_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/24 (1947 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.153 0.077 199.8 86: (ns/day) (hour/ns) 86: Performance: 19.129 1.255 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.401 0.200 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.326 3.276 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_25_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/25 (1877 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: 86: WARNING 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There were 2 WARNINGs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.369 0.185 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.960 3.015 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.329 0.165 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.918 2.691 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_26_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/26 (1751 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: The Berendsen thermostat does not generate the correct kinetic energy 86: distribution, and should not be used for new production simulations (in 86: our opinion). We would recommend the V-rescale thermostat. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 3 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.346 0.173 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.494 2.826 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.318 0.159 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.237 2.598 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_27_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/27 (1551 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.285 0.143 199.9 86: (ns/day) (hour/ns) 86: Performance: 10.305 2.329 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.325 0.163 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.038 2.656 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_28_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/28 (1476 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.299 0.150 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.809 2.447 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.304 0.152 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.647 2.488 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_29_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/29 (1439 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: 86: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: The Berendsen barostat does not generate any strictly correct ensemble, 86: and should not be used for new production simulations (in our opinion). 86: We recommend using the C-rescale barostat instead. 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: 86: There was 1 WARNING 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.310 0.155 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.461 2.537 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.344 0.172 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.535 2.812 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_30_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/30 (1596 ms) 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 86: 1 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Number of degrees of freedom in T-Coupling group System is 27.00 86: 86: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_input.mdp]: 86: You are using a plain Coulomb cut-off, which might produce artifacts. 86: You might want to consider using PME electrostatics. 86: 86: 86: 86: There were 4 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.308 0.154 199.9 86: (ns/day) (hour/ns) 86: Performance: 9.532 2.518 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Changing nstlist from 8 to 20, rlist from 0.764 to 0.88 86: 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.340 0.170 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.647 2.775 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_31_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/31 (1480 ms) 86: [----------] 32 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (28556 ms total) 86: 86: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest 86: [ RUN ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'FirstWaterMolecule' has 3 atoms 86: Pull group 2 'SecondWaterMolecule' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 9.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 2573.591 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 1.112 nm 1.000 nm 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.386 0.193 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.612 3.153 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: NOTE: 10 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.418 0.209 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.025 3.417 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModularPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest.WithinTolerances/0 (448 ms) 86: [----------] 1 test from SimulatorsAreEquivalentDefaultModularPull/SimulatorComparisonTest (448 ms total) 86: 86: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest 86: [ RUN ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 86: that with the Verlet scheme, nstlist has no effect on the accuracy of 86: your simulation. 86: 86: 86: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: Setting nstcalcenergy (100) equal to nstenergy (4) 86: 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'FirstWaterMolecule' has 3 atoms 86: Pull group 2 'SecondWaterMolecule' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 9.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 2573.591 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 1.112 nm 1.000 nm 86: 86: There were 3 NOTEs 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: Generated 3 of the 3 non-bonded parameter combinations 86: 86: Generated 3 of the 3 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 12 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.246 0.123 199.9 86: (ns/day) (hour/ns) 86: Performance: 11.920 2.013 86: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI thread 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 16 steps, 0.0 ps. 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.235 0.118 199.9 86: (ns/day) (hour/ns) 86: Performance: 12.483 1.923 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file 86: Opened /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacyPull_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 86: 86: [ OK ] SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest.WithinTolerances/0 (275 ms) 86: [----------] 1 test from SimulatorsAreEquivalentDefaultLegacyPull/SimulatorComparisonTest (275 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 94 tests from 4 test suites ran. (66074 ms total) 86: [ PASSED ] 94 tests. 86/87 Test #86: MdrunSimulatorComparison .................. Passed 66.11 sec test 87 Start 87: MdrunVirtualSiteTests 87: Test command: /build/reproducible-path/gromacs-2024.4/build/basic-dp/bin/mdrun-vsites-test "-ntmpi" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/basic-dp/Testing/Temporary/MdrunVirtualSiteTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 37 tests from 2 test suites. 87: [----------] Global test environment set-up. 87: [----------] 1 test from VirtualSiteVelocityTest 87: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 87: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 87: [----------] 1 test from VirtualSiteVelocityTest (0 ms total) 87: 87: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 21.2%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 7.5%. 87: 87: NOTE: 7.5 % of the available CPU time was lost due to load imbalance 87: in the domain decomposition. 87: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 87: You can also consider manually changing the decomposition (option -dd); 87: e.g. by using fewer domains along the box dimension in which there is 87: considerable inhomogeneity in the simulated system. 87: 87: NOTE: 23 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 9 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.108 1.090 193.4 87: (ns/day) (hour/ns) 87: Performance: 0.713 33.638 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: trr version: GMX_trn_file (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (2486 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.7%. 87: The balanceable part of the MD step is 39%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 1.0%. 87: 87: 87: NOTE: 34 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 192.0 87: (ns/day) (hour/ns) 87: Performance: 634.593 0.038 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (87 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 36%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 819.470 0.029 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (580 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.4 87: (ns/day) (hour/ns) 87: Performance: 963.370 0.025 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (280 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 936.537 0.026 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (271 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 30 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 896.260 0.027 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (144 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 20 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 11 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 1.790 0.949 188.7 87: (ns/day) (hour/ns) 87: Performance: 0.820 29.280 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (2253 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 13 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 11 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 2.352 1.218 193.1 87: (ns/day) (hour/ns) 87: Performance: 0.638 37.591 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (2723 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 87: 1 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 5 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.9 87: (ns/day) (hour/ns) 87: Performance: 971.115 0.025 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (273 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.1%. 87: The balanceable part of the MD step is 40%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.8%. 87: 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.0 87: (ns/day) (hour/ns) 87: Performance: 907.356 0.026 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (1084 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: 87: Dynamic load balancing report: 87: DLB was off during the run due to low measured imbalance. 87: Average load imbalance: 2.7%. 87: The balanceable part of the MD step is 0%, load imbalance is computed from this. 87: Part of the total run time spent waiting due to load imbalance: 0.0%. 87: 87: 87: NOTE: 65 % of the run time was spent in domain decomposition, 87: 0 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: NOTE: 11 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.794 0.397 200.0 87: (ns/day) (hour/ns) 87: Performance: 1.959 12.254 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (2208 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 187.6 87: (ns/day) (hour/ns) 87: Performance: 872.523 0.028 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (1147 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 915.121 0.026 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (311 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.7 87: (ns/day) (hour/ns) 87: Performance: 865.576 0.028 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (59 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 27 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 188.2 87: (ns/day) (hour/ns) 87: Performance: 870.195 0.028 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (112 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.021 0.011 199.1 87: (ns/day) (hour/ns) 87: Performance: 72.720 0.330 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (67 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 940.182 0.026 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (76 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 50, rlist from 0.713 to 0.805 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 29 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.5 87: (ns/day) (hour/ns) 87: Performance: 948.659 0.025 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (151 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 190.3 87: (ns/day) (hour/ns) 87: Performance: 864.773 0.028 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (151 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.4 87: (ns/day) (hour/ns) 87: Performance: 914.608 0.026 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (693 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: Setting nstcalcenergy (100) equal to nstenergy (4) 87: 87: Number of degrees of freedom in T-Coupling group System is 45.00 87: 87: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: There are 6 non-linear virtual site constructions. Their contribution to 87: the energy error is approximated. In most cases this does not affect the 87: error significantly. 87: 87: 87: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 87: You are using a plain Coulomb cut-off, which might produce artifacts. 87: You might want to consider using PME electrostatics. 87: 87: 87: 87: There were 4 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Changing nstlist from 8 to 100, rlist from 0.729 to 0.81 87: 87: Update groups can not be used for this system because an incompatible virtual site type is used 87: 87: Using 2 MPI threads 87: Using 1 OpenMP thread per tMPI thread 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Virtual sites test system in vacuo' 87: 8 steps, 0.0 ps. 87: Generated 3 of the 6 non-bonded parameter combinations 87: 87: Excluding 3 bonded neighbours molecule type 'VSTEST' 87: 87: Cleaning up constraints and constant bonded interactions with virtual sites 87: 87: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 87: 87: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 87: 87: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 87: 87: Note that mdrun will redetermine rlist based on the actual pair-list setup 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 28 % of the run time was spent communicating energies, 87: you might want to increase some nst* mdp options 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.002 0.001 189.6 87: (ns/day) (hour/ns) 87: Performance: 870.427 0.028 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: Reading file /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (double precision) 87: 87: Reading virtual site types... 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (1546 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 87: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 87: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 87: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (16714 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 37 tests from 2 test suites ran. (16730 ms total) 87: [ PASSED ] 37 tests. 87/87 Test #87: MdrunVirtualSiteTests ..................... Passed 16.77 sec 100% tests passed, 0 tests failed out of 87 Label Time Summary: GTest = 1969.82 sec*proc (85 tests) IntegrationTest = 990.85 sec*proc (28 tests) MpiTest = 1500.16 sec*proc (21 tests) QuickGpuTest = 298.40 sec*proc (20 tests) SlowGpuTest = 1606.96 sec*proc (14 tests) SlowTest = 955.50 sec*proc (13 tests) UnitTest = 23.48 sec*proc (44 tests) Total Test time (real) = 932.37 sec touch build-basic dh_testdir LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/mpi/lib /usr/bin/make -j12 -C build/mpi make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi 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'/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/pthreads.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvaratoms.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target thread_mpi cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/nonbonded_bench.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwt.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/coder.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/dict.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/fixpoint.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/huffman.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target energyanalysis cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_alb.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/huffmem.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/lz77.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/merge_sort.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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'/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target scanner cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/sparsematrix.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 2%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_apath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_apath.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/timeunitmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/treesupport.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_distances.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_gpath.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_gpath.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_neuralnetwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_neuralnetwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_protein.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_rotations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_rotations.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_volmaps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_volmaps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullcoordexpressionparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/transformationcoordinate.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 4%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -MF CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o.d -o CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidesimulationworkload.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -MF CMakeFiles/taskassignment.dir/findallgputasks.cpp.o.d -o CMakeFiles/taskassignment.dir/findallgputasks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/compositesimulatorelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -MF CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/expandedensembleelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 8%] Built target colvars_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/mttk.cpp.o -MF CMakeFiles/modularsimulator.dir/mttk.cpp.o.d -o CMakeFiles/modularsimulator.dir/mttk.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/mttk.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 8%] Built target taskassignment cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -MF CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/coolstuff.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/exceptions.cpp In file included from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:87: /build/reproducible-path/gromacs-2024.4/build/mpi/src/include/buildinfo.h:73:9: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.11.0" | ^~~~~~~~~~~~~ In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:62: /usr/include/aarch64-linux-gnu/hwloc/autogen/config.h:15:9: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.11.2" | ^~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fileredirector.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -MF CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/keyvaluetreetransform.cpp cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/loggerbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/path.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -MF CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/pleasecite.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -MF CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/programcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -MF CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/strconvert.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/strdb.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/sycl_version_information.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernel_common.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/pairlistwork.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/prunekerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/simd_prune_kernel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_prune_kernel.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/reversetopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -MF CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o.d -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/com.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc_simd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbcenums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/seed.cpp.o -MF CMakeFiles/libgromacs.dir/random/seed.cpp.o.d -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -MF CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tabulatednormaldistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/manager.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -MF CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o.d -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -MF CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/atomsbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/block.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/ifunc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/swap/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/edsam.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_angle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_awh.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_bundle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_chi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dipoles.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_disre.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dos.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dyecoupl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_enemat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_energy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmtraj.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_order.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_polystat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_potential.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_principal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rotacf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sorient.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_spatial.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_spol.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_tcaf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_xpm2ps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/add_par.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c 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CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/modules/displacement.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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&& /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/forcerec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/gpuforcereduction_impl_stubs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/shake.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wholemoleculetransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/orires.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/pairs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -MF CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o.d -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/position_restraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/long_range_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gather.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/md.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/md.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/mdmodules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/membedholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/membedholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/mimic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/minimize.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/rerun.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationcontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/printtime.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/confio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/groio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/matio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/matio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/md5.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/md5.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/mrcdensitymap.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectionoptionbehavior.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_same.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi.so.9 -o ../../lib/libgromacs_mpi.so.9.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -lmuparser cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi.so.9.0.0 ../../lib/libgromacs_mpi.so.9 ../../lib/libgromacs_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/box.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/integrator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdmodule.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_mpi ../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2024.4/api/nblib/particlesequencer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 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/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_mpi.so.0 -o ../../lib/libgmxapi_mpi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi.so.0.4.0 ../../lib/libgmxapi_mpi.so.0 ../../lib/libgmxapi_mpi.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/launch_0_2_1.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/module.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -MF CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o.d -o CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp/sessionresources.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/export_context.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/export_system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/export_tprfile.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pycontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_resources.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_resources.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_resources.a CMakeFiles/gmxapi_extension_resources.dir/sessionresources.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_resources.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target gmxapi_extension_resources /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -MF CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o.d -o CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp/ensemblepotential.cpp /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp: In lambda function: /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:131:26: warning: 'void pybind11::exception::operator()(const char*) const [with type = gmxpy::Exception]' is deprecated: Please use py::set_error() instead (https://github.com/pybind/pybind11/pull/4772) [-Wdeprecated-declarations] 131 | baseException(message.c_str()); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.h:51, from /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:49: /usr/include/pybind11/pybind11.h:2625:10: note: declared here 2625 | void operator()(const char *message) const { set_error(*this, message); } | ^~~~~~~~ /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:137:29: warning: 'void pybind11::exception::operator()(const char*) const [with type = gmxpy::detail::export_exceptions(pybind11::module&)::UnknownExceptionPlaceHolder]' is deprecated: Please use py::set_error() instead (https://github.com/pybind/pybind11/pull/4772) [-Wdeprecated-declarations] 137 | unknownException(message.c_str()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/pybind11/pybind11.h:2625:10: note: declared here 2625 | void operator()(const char *message) const { set_error(*this, message); } | ^~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pysystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/wrapped_exceptions_0_3_1.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/mpi_bindings.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_ensemblepotential.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_ensemblepotential.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_ensemblepotential.a CMakeFiles/gmxapi_extension_ensemblepotential.dir/ensemblepotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_ensemblepotential.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target gmxapi_extension_ensemblepotential /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -MF CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o.d -o CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp/nullpotential.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pycontext_create.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/mpi_gromacs_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -P CMakeFiles/gmxapi_extension_test.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_test.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libgmxapi_extension_test.a CMakeFiles/gmxapi_extension_test.dir/nullpotential.cpp.o /usr/bin/ranlib ../../../../lib/libgmxapi_extension_test.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target gmxapi_extension_test /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /usr/include/python3.12 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -MF CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o.d -o CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/pythonmodule/export_plugin.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/_gmxapi.dir/link.txt --verbose=1 lto-wrapper: warning: using serial compilation of 4 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension.dir/link.txt --verbose=1 lto-wrapper: warning: using serial compilation of 3 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file,CMakeFiles/gmxapi_extension.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../lib/myplugin.cpython-312-aarch64-linux-gnu.so CMakeFiles/gmxapi_extension.dir/export_plugin.cpp.o ../../../../lib/libgmxapi_extension_ensemblepotential.a ../../../../lib/libgmxapi_extension_test.a ../../../../lib/libgmxapi_extension_resources.a ../../../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi/lib cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule && /usr/bin/strip /build/reproducible-path/gromacs-2024.4/build/mpi/lib/myplugin.cpython-312-aarch64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target gmxapi_extension /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -Wl,--dependency-file,CMakeFiles/_gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o gmxapi_staging/gmxapi/_gmxapi.cpython-312-aarch64-linux-gnu.so CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_gromacs_support.cpp.o ../../lib/libgmxapi_mpi.so.0.4.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi/lib cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi && /usr/bin/strip /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/gmxapi_staging/gmxapi/_gmxapi.cpython-312-aarch64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target _gmxapi cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f 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-I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -MF CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o.d -o CMakeFiles/methane-water-integration.dir/methane-water-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/methane-water-integration.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/argon-forces-integration.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/argon-forces-integration.dir/link.txt --verbose=1 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'/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -j12 -C build/mpi-dp make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/mpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parser.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/selection && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/scanner.cpp.o -MF CMakeFiles/scanner.dir/scanner.cpp.o.d -o CMakeFiles/scanner.dir/scanner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner.cpp /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/errhandler.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/tmpi_malloc.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -MF CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o.d -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/lmfit/lmmin.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/atomic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwlzh.c /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/bwt.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -MF CMakeFiles/linearalgebra.dir/eigensolver.cpp.o.d -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/eigensolver.cpp [ 0%] Built target release-version-info make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoption.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/lock.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/pthreads.cpp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractsection.cpp.o -MF CMakeFiles/options.dir/abstractsection.cpp.o.d -o CMakeFiles/options.dir/abstractsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractsection.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/coder.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 2%] Built target thread_mpi /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -MF CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o.d -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers 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src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/mtf.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/rle.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/legacymodules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/tng_compress.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/vals16.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc2.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc3.c [ 2%] Built target lmfit_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 2%] Built target energyanalysis cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o -MF CMakeFiles/linearalgebra.dir/matrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/behaviorcollection.cpp.o -MF CMakeFiles/options.dir/behaviorcollection.cpp.o.d -o CMakeFiles/options.dir/behaviorcollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/behaviorcollection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/nonbonded_bench.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 2%] Built target gmx_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoption.cpp.o -MF CMakeFiles/options.dir/filenameoption.cpp.o.d -o CMakeFiles/options.dir/filenameoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicc -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-stringop-truncation -MD -MT src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -MF CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o.d -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar_neuralnetworkcompute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvar_neuralnetworkcompute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvaratoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvaratoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 2%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_abf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_abf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsassigner.cpp.o -MF CMakeFiles/options.dir/optionsassigner.cpp.o.d -o CMakeFiles/options.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsassigner.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsection.cpp.o -MF CMakeFiles/options.dir/optionsection.cpp.o.d -o CMakeFiles/options.dir/optionsection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/timeunitmanager.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 4%] Built target linearalgebra /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/treesupport.cpp.o -MF CMakeFiles/options.dir/treesupport.cpp.o.d -o CMakeFiles/options.dir/treesupport.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/treesupport.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_alb.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 4%] Built target scanner cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull.cpp.o -MF CMakeFiles/pulling.dir/pull.cpp.o.d -o CMakeFiles/pulling.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -MF CMakeFiles/pulling.dir/transformationcoordinate.cpp.o.d -o CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/transformationcoordinate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_histogram_reweight_amd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_histogram_reweight_amd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_meta.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_meta.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_restraint.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_alchlambda.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_alchlambda.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 8%] Built target options cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fopenmp -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_protein.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_protein.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/andersentemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/andersentemperaturecoupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -MF CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/checkpointhelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/expandedensembleelement.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 10%] Built target taskassignment cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -MF CMakeFiles/modularsimulator.dir/topologyholder.cpp.o.d -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/topologyholder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -MF CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/trajectoryelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 16%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/mpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/alignedallocator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/any.cpp.o -MF CMakeFiles/libgromacs.dir/utility/any.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/any.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -MF CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/basenetwork.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -MF CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -MF CMakeFiles/libgromacs.dir/utility/booltype.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/booltype.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/compare.cpp.o -MF CMakeFiles/libgromacs.dir/utility/compare.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -MF CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/cstringutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -MF CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -MF CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/exceptions.cpp In file included from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:87: /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include/buildinfo.h:73:9: warning: "HWLOC_VERSION" redefined 73 | #define HWLOC_VERSION "2.11.0" | ^~~~~~~~~~~~~ In file included from /usr/include/hwloc.h:56, from /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/binaryinformation.cpp:62: /usr/include/aarch64-linux-gnu/hwloc/autogen/config.h:15:9: note: this is the location of the previous definition 15 | #define HWLOC_VERSION "2.11.2" | ^~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -MF CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/fatalerror.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/logger.cpp.o -MF CMakeFiles/libgromacs.dir/utility/logger.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/logger.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/loggerbuilder.cpp cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -MF CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/message_string_collector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/message_string_collector.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/mpiinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/mpiinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -MF CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -MF CMakeFiles/libgromacs.dir/utility/strdb.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -MF CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sycl_version_information.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -MF CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/sysinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textreader.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/textreader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -MF CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/textwriter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -MF CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/txtdump.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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-Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/benchmark/bench_system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/exclusionchecker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/exclusionchecker.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/freeenergydispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/freeenergydispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kerneldispatch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_geometry.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o.d -o 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/pargs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/shellcompletions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -MF CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o.d -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/viewit.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/atomdistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/box.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/box.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/box.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/cellsizes.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/collect.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/collect.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/computemultibodycutoffs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/computemultibodycutoffs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/distribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlb.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_constraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/dump.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dump.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/ga2la.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomset.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localatomsetmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/localtopologychecker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopologychecker.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/makebondedlinks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/makebondedlinks.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/mdsetup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/nsgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/nsgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/partition.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/partition.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/redistribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/reversetopology.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -MF CMakeFiles/libgromacs.dir/domdec/utility.cpp.o.d -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/utility.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -MF CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o.d -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/3dtransforms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -MF CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o.d -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfit.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -MF CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o.d -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/densityfittingforce.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -MF CMakeFiles/libgromacs.dir/math/do_fit.cpp.o.d -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/do_fit.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -MF CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o.d -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/functions.cpp.o -MF CMakeFiles/libgromacs.dir/math/functions.cpp.o.d -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/functions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -MF CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o.d -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/gausstransform.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/invertmatrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/matrix.cpp.o -MF CMakeFiles/libgromacs.dir/math/matrix.cpp.o.d -o CMakeFiles/libgromacs.dir/math/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -MF CMakeFiles/libgromacs.dir/math/neldermead.cpp.o.d -o CMakeFiles/libgromacs.dir/math/neldermead.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/neldermead.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -MF CMakeFiles/libgromacs.dir/math/nrjac.cpp.o.d -o CMakeFiles/libgromacs.dir/math/nrjac.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/optimization.cpp.o -MF CMakeFiles/libgromacs.dir/math/optimization.cpp.o.d -o CMakeFiles/libgromacs.dir/math/optimization.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/math/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -MF CMakeFiles/libgromacs.dir/math/veccompare.cpp.o.d -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -MF CMakeFiles/libgromacs.dir/math/vecdump.cpp.o.d -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/awh_history.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/checkpointdata.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/commrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/df_history.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/energyhistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/forcebuffers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/forcebuffers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/group.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/inputrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/interaction_const.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/interaction_const.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/md_enums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/multipletimestepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/multipletimestepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observableshistory.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/observablesreducer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -MF CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o.d -o CMakeFiles/libgromacs.dir/mdtypes/threaded_force_buffer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/threaded_force_buffer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbcmethods.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -MF CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o.d -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/rmpbc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -MF CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o.d -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/splineutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -MF CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/cyclecounter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -MF CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/wallcycle.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -MF CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o.d -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/walltime_accounting.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atoms.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/block.cpp.o -MF CMakeFiles/libgromacs.dir/topology/block.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -MF CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -MF CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/forcefieldparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/idef.cpp.o -MF CMakeFiles/libgromacs.dir/topology/idef.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -MF CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/index.cpp.o -MF CMakeFiles/libgromacs.dir/topology/index.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/index.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -MF CMakeFiles/libgromacs.dir/topology/invblock.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/invblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_atomloops.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -MF CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/mtop_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -MF CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/residuetypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -MF CMakeFiles/libgromacs.dir/topology/symtab.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topology.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topology.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -MF CMakeFiles/libgromacs.dir/topology/topsort.cpp.o.d -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -MF CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -MF CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o.d -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -MF CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o.d -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imd.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imd.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -MF CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o.d -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/imd/imdsocket.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/communicator_stub.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/communicator_stub.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -MF CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/anadih.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/angle_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/binsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cluster_methods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/cluster_methods.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/cmat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/dens_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/dlist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/eigio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/fitahx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_cluster.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_clustsize.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_confrms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_density.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_filter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_gyrate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_h2order.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_hbond.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_helix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_helixorient.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_hydorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_lie.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_make_edi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_mdmat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmeig.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_nmens.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rama.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsdist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_rmsf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_saxs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sham.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_sigeps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_traj.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_trjorder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_vanhove.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_velacc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wheel.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/nrama.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/princ.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/sfactor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/thermochemistry.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/calch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/convparm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/editconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/fflibutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/gen_ad.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/gen_vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/h_db.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hackblock.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/hizzie.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/insert_molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -MF CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -MF 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -MF CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o.d -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/polynomials.cpp cd 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -MF CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o.d -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o.d -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/datamodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -MF CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o.d -o 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/outputadapters/setprecision.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -MF CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o.d -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/outputadapters/setstarttime.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/trjcat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -MF CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/trjconv.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -MF CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o.d -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tune_pme.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -MF CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/conformation_utilities.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/calcmu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/calcvir.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/compute_io.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraint_gpu_helpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraint_gpu_helpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraintrange.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/coupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/dispersioncorrection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/ebin.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/enerdata_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/expanded.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/force.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/gmx_omp_nthreads.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/gpuforcereduction_impl_stubs.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/groupcoord.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/md_support.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdebin_bar.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdgraph_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdoutf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/membed.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/perf_est.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/rbin.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/resethandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sighandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/sim_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/simulationsignal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/splitter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/stat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/stophandler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tgroup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_gpu_impl_stubs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_impl_stubs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/update_vv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_vv.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroupscog.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vcm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/vsite.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/wall.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o -MF CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o.d -o CMakeFiles/libgromacs.dir/mdlib/wholemoleculetransform.cpp.o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/awh.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/awh.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasgrid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasparams.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasparams.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biassharing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biassharing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/biasstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/correlationtensor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationtensor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/awh/pointstate.cpp.o -c 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/densityfittingoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingoutputprovider.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include 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-fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting/densityfittingparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/densityfittingparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmminputgenerator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -MF CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o.d -o CMakeFiles/libgromacs.dir/applied_forces/qmmm/qmmm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/calculate_spline_moduli.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/ewald.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/ewald_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_grid.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_load_balancing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_redistribute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_solve.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spline_work.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spread.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o.d -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -MF CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o.d -o 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -MF CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o.d -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/fft_fftw3.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/hostallocator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/gpueventsynchronizer_helpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer_helpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/nvshmem_utils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/nvshmem_utils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_context.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_context.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/device_stream.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_stream.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -MF CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o.d -o CMakeFiles/libgromacs.dir/gpu_utils/pmalloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/cpuinfo.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/detecthardware.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/device_management_common.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_common.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -MF CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o.d -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacysimulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulationinputhandle.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/simulatorbuilder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -MF CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/tpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/freeenergy.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/handlerestart.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/logging.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -MF CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodulesnotifiers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -MF 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CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o.d -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -MF CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o.d -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/espio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/espio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/filetypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tngio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tpxio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/trrio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/trxio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/writeps.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xdrd.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xtcio.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/xvgr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -MF CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/centerofmass.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -MF CMakeFiles/libgromacs.dir/selection/compiler.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -MF CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -MF CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/indexutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -MF CMakeFiles/libgromacs.dir/selection/mempool.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/mempool.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -MF CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/nbsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/params.cpp.o -MF CMakeFiles/libgromacs.dir/selection/params.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/params.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -MF CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parsetree.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -MF CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/poscalc.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/position.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -MF CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/scanner_internal.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/selection.cpp.o -MF CMakeFiles/libgromacs.dir/selection/selection.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_compare.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_keywords.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_merge.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_permute.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -MF CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_simple.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/mpi-dp/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -MF CMakeFiles/libgromacs.dir/selection/symrec.cpp.o.d -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/symrec.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/libgromacs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_mpi_d.so.9 -o ../../lib/libgromacs_mpi_d.so.9.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 -lmuparser cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_mpi_d.so.9.0.0 ../../lib/libgromacs_mpi_d.so.9 ../../lib/libgromacs_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/box.cpp.o -MF CMakeFiles/nblib.dir/box.cpp.o.d -o CMakeFiles/nblib.dir/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/box.cpp make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -MF CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o.d -o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/gmxcalculatorcpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/integrator.cpp.o -MF CMakeFiles/nblib.dir/integrator.cpp.o.d -o CMakeFiles/nblib.dir/integrator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/integrator.cpp make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/resourceassignment.cpp /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/interactions.cpp.o -MF CMakeFiles/nblib.dir/interactions.cpp.o.d -o CMakeFiles/nblib.dir/interactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/interactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/context.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/context.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/context.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/context.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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api/nblib/CMakeFiles/nblib.dir/molecules.cpp.o -MF CMakeFiles/nblib.dir/molecules.cpp.o.d -o CMakeFiles/nblib.dir/molecules.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/molecules.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include 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-fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -MF CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o.d -o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/nbnxmsetuphelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/gmxapi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particlesequencer.cpp.o -MF CMakeFiles/nblib.dir/particlesequencer.cpp.o.d -o CMakeFiles/nblib.dir/particlesequencer.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/particlesequencer.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmx.dir/link.d CMakeFiles/gmx_objlib.dir/gmx.cpp.o CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/gmx_mpi_d ../../lib/libgromacs_mpi_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 95%] Built target gmx cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/md.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/md.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/md.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/md.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include 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-Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/mdsignals.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/session.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/session.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/session.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/session.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/particletype.cpp.o -MF CMakeFiles/nblib.dir/particletype.cpp.o.d -o CMakeFiles/nblib.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/particletype.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/status.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/status.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/simulationstate.cpp.o -MF CMakeFiles/nblib.dir/simulationstate.cpp.o.d -o CMakeFiles/nblib.dir/simulationstate.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/simulationstate.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/system.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/system.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/version.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/version.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topologyhelpers.cpp.o -MF CMakeFiles/nblib.dir/topologyhelpers.cpp.o.d -o CMakeFiles/nblib.dir/topologyhelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/topologyhelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/topology.cpp.o -MF CMakeFiles/nblib.dir/topology.cpp.o.d -o CMakeFiles/nblib.dir/topology.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/tpr.cpp.o -MF CMakeFiles/nblib.dir/tpr.cpp.o.d -o CMakeFiles/nblib.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/virials.cpp.o -MF CMakeFiles/nblib.dir/virials.cpp.o.d -o CMakeFiles/nblib.dir/virials.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/virials.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/calculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/transformations.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -MF CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o.d -o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/convertGmxToNblib.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/mpicxx -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -Dnblib_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -Wno-cast-function-type-strict -MD -MT api/nblib/CMakeFiles/nblib.dir/util/setup.cpp.o -MF CMakeFiles/nblib.dir/util/setup.cpp.o.d -o CMakeFiles/nblib.dir/util/setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_mpi_d.so.0 -o ../../lib/libgmxapi_mpi_d.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o ../../lib/libgromacs_mpi_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi_mpi_d.so.0.4.0 ../../lib/libgmxapi_mpi_d.so.0 ../../lib/libgmxapi_mpi_d.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 97%] Built target gmxapi cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/nblib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libnblib_gmx.so.0 -o ../../lib/libnblib_gmx.so.0.1.0 CMakeFiles/nblib.dir/box.cpp.o CMakeFiles/nblib.dir/gmxcalculatorcpu.cpp.o CMakeFiles/nblib.dir/integrator.cpp.o CMakeFiles/nblib.dir/interactions.cpp.o CMakeFiles/nblib.dir/molecules.cpp.o CMakeFiles/nblib.dir/nbnxmsetuphelpers.cpp.o CMakeFiles/nblib.dir/particlesequencer.cpp.o CMakeFiles/nblib.dir/particletype.cpp.o CMakeFiles/nblib.dir/simulationstate.cpp.o CMakeFiles/nblib.dir/topologyhelpers.cpp.o CMakeFiles/nblib.dir/topology.cpp.o CMakeFiles/nblib.dir/tpr.cpp.o CMakeFiles/nblib.dir/virials.cpp.o CMakeFiles/nblib.dir/listed_forces/calculator.cpp.o CMakeFiles/nblib.dir/listed_forces/transformations.cpp.o CMakeFiles/nblib.dir/listed_forces/conversions.cpp.o CMakeFiles/nblib.dir/listed_forces/convertGmxToNblib.cpp.o CMakeFiles/nblib.dir/util/setup.cpp.o -lm ../../lib/libgromacs_mpi_d.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib && /usr/bin/cmake -E cmake_symlink_library ../../lib/libnblib_gmx.so.0.1.0 ../../lib/libnblib_gmx.so.0 ../../lib/libnblib_gmx.so make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [100%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=1 -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/legacy/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fopenmp -MD -MT api/nblib/samples/CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -MF CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o.d -o CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/samples/argon-forces-integration.cpp /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples && /usr/bin/mpicxx -DGMX_DOUBLE=1 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--verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/argon-forces-integration.dir/link.d "CMakeFiles/argon-forces-integration.dir/argon-forces-integration.cpp.o" -o ../../../bin/argon-forces-integration ../../../lib/libnblib_gmx.so.0.1.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi-dp/lib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [100%] Built target argon-forces-integration cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples && /usr/bin/cmake -E cmake_link_script CMakeFiles/methane-water-integration.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 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'/build/reproducible-path/gromacs-2024.4/build/mpi-dp' LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/mpi/lib /usr/bin/make -j12 -C build/mpi tests make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles 77 /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/mpi && 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest.dir/build [ 5%] Built target energyanalysis make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -Dgtest_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -I/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/src/gtest-all.cc [ 5%] Built target mdrun_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 5%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 5%] Built target taskassignment [ 6%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 55%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build [ 55%] Built target gmx /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/DependInfo.cmake "--color=" [ 55%] Built target gmxapi /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend [ 57%] Built target nblib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_spc2_water_box.dir/build cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests && /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmx_mpi -quiet grompp -f /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp -c /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2.gro -p /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2.top /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmxapi_extension_resources make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" [ 58%] Built target methane-water-integration [ 58%] Built target argon-forces-integration make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmxapi_extension_ensemblepotential Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 9.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: NVE simulation: will use the initial temperature of 2573.591 K for determining the Verlet buffer size NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/grompp.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 2 NOTEs Setting the LD random seed to -810059155 Generated 3 of the 3 non-bonded parameter combinations Generated 3 of the 3 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Analysing residue names: There are: 2 Water residues Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmxapi_extension_spc2_water_box cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gtest.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so.1.13.0 -o ../../../../lib/libgtest.so.1.13.0 "CMakeFiles/gtest.dir/src/gtest-all.cc.o" cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgtest.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gtest /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/depend /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build.make src/external/googletest/googletest/CMakeFiles/gtest_main.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -Dgtest_main_EXPORTS -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fPIC -Wall -Wshadow -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -MD -MT src/external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/src/gtest_main.cc make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 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CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/src/gmock-all.cc cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gtest_main.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest_main.so.1.13.0 -o ../../../../lib/libgtest_main.so.1.13.0 CMakeFiles/gtest_main.dir/src/gtest_main.cc.o ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googletest && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so.1.13.0 ../../../../lib/libgtest_main.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gtest_main /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/depend /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/build.make python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -MF CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o.d -o CMakeFiles/gmxapi_extension_histogram-test.dir/test_histogram.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests/test_histogram.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/build.make 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fvisibility=hidden -MD -MT python_packaging/sample_restraint/tests/CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -MF CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o.d -o CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/tests/test_bounding_restraint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi_extension_histogram-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 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CMakeFiles/gmxapi_extension_bounding-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi_extension_bounding-test.dir/link.d "CMakeFiles/gmxapi_extension_bounding-test.dir/test_bounding_restraint.cpp.o" -o ../../../bin/gmxapi_extension_bounding-test ../../../lib/libgmxapi_extension_ensemblepotential.a ../../../lib/libgtest_main.so.1.13.0 ../../../lib/libgmxapi_extension_resources.a ../../../lib/libgmxapi_mpi.so.0.4.0 ../../../lib/libgtest.so.1.13.0 -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/mpi/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmxapi_extension_bounding-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/mpicxx -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,--dependency-file,CMakeFiles/gmock.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so.1.13.0 -o ../../../../lib/libgmock.so.1.13.0 "CMakeFiles/gmock.dir/src/gmock-all.cc.o" ../../../../lib/libgtest.so.1.13.0 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgmock.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 58%] Built target gmock /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/testutils /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/CMakeFiles/testutils.dir/cmdlinetest.cpp.o -MF CMakeFiles/testutils.dir/cmdlinetest.cpp.o.d -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/cmdlinetest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/calc_verletbuf.cpp /usr/bin/make -f src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/awh_setup.cpp.o -MF CMakeFiles/awh-test.dir/awh_setup.cpp.o.d -o CMakeFiles/awh-test.dir/awh_setup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/build.make src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-mpi-test.dir/link.d "CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o" "CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 59%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/build.make src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -MF 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/calcvir.cpp.o -MF CMakeFiles/mdlib-test.dir/calcvir.cpp.o.d -o CMakeFiles/mdlib-test.dir/calcvir.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/calcvir.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testutils-mpi-test.dir/link.d "CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o" "CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 59%] Built target testutils-mpi-test /usr/bin/make -f src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/build.make 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directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvars.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvars.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -MF CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/testasserts_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingamplitudelookup.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmtopologypreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/arrayref.cpp.o -MF CMakeFiles/utility-test.dir/arrayref.cpp.o.d -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/arrayref.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/bias.cpp.o -MF CMakeFiles/awh-test.dir/bias.cpp.o.d -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/bias.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -P CMakeFiles/nblib_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libnblib_test_infrastructure.a CMakeFiles/nblib_test_infrastructure.dir/testsystems.cpp.o CMakeFiles/nblib_test_infrastructure.dir/__/__/__/src/testutils/unittest_main.cpp.o /usr/bin/ranlib ../../../lib/libnblib_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 59%] Built target nblib_test_infrastructure /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -MF CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o.d -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/tests/xvgtest_tests.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/densityfitting/tests/densityfittingforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/testutils/tests/CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -MF CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o.d -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmoptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/simulatorcomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o /usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 61%] Built target mdrun_test_infrastructure /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build.make src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" 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src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -MF CMakeFiles/nbnxm-test.dir/exclusions.cpp.o.d -o CMakeFiles/nbnxm-test.dir/exclusions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/exclusions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/ebin.cpp.o -MF CMakeFiles/mdlib-test.dir/ebin.cpp.o.d -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/ebin.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/testutils-test.dir/link.d "CMakeFiles/testutils-test.dir/interactivetest.cpp.o" "CMakeFiles/testutils-test.dir/refdata_tests.cpp.o" "CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o" "CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o" "CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o" -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libtestutils.a ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 61%] Built target testutils-test /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 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-DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -MF CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o.d -o CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energydrifttracker.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -MF CMakeFiles/mdlib-test.dir/energyoutput.cpp.o.d -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/energyoutput.cpp /usr/bin/mpicxx -g -O2 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src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/hashedmap.cpp.o -MF CMakeFiles/domdec-test.dir/hashedmap.cpp.o.d -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/hashedmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxlib/nonbonded/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxlib/nonbonded/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarspreprocessor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarspreprocessor.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxlib/nonbonded/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nonbonded-fep-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -MF CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o.d -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/localatomsetmanager.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nonbonded-fep-test.dir/link.d "CMakeFiles/nonbonded-fep-test.dir/nb_free_energy.cpp.o" "CMakeFiles/nonbonded-fep-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/nonbonded-fep-test ../../../../../lib/libtestutils.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 -lm ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 61%] Built target nonbonded-fep-test /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -MF CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o.d -o CMakeFiles/domdec-mpi-test.dir/haloexchange_mpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/tests/haloexchange_mpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -DGMX_CP2K=0 -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmmforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/nbnxm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/nbnxm/tests/CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -MF CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o.d -o CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a "CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o" "CMakeFiles/onlinehelp-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 62%] Built target onlinehelp-test-shared /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -MF CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o.d -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/pairs.cpp.o -MF CMakeFiles/listed_forces-test.dir/pairs.cpp.o.d -o CMakeFiles/listed_forces-test.dir/pairs.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/awh/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/awh/tests/CMakeFiles/awh-test.dir/biassharing.cpp.o -MF CMakeFiles/awh-test.dir/biassharing.cpp.o.d -o CMakeFiles/awh-test.dir/biassharing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biassharing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/densityfitting/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/densityfitting/tests/CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/qmmm/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/qmmm/tests/CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -MF CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o.d -o CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/tests/qmmm.cpp /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp: In function 'std::pair gmx::test::{anonymous}::combineLJParams(real, real, real, real, LJCombinationRule)': /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:186:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 186 | const LJCombinationRule ljCombinationRule) | ^ cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/colvarsforceprovider.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsforceprovider.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -MF CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o.d -o CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/freeenergyparameters.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/density_fitting_applied_forces-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/density_fitting_applied_forces-test.dir/link.d "CMakeFiles/density_fitting_applied_forces-test.dir/densityfitting.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingamplitudelookup.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingforceprovider.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/densityfittingoptions.cpp.o" "CMakeFiles/density_fitting_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/density_fitting_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 63%] Built target density_fitting_applied_forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests /build/reproducible-path/gromacs-2024.4/build/mpi 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make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -MF CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_stream_manager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/colvars/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/applied_forces/colvars/tests/CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/colvars_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/qmmm_applied_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/qmmm_applied_forces-test.dir/link.d "CMakeFiles/qmmm_applied_forces-test.dir/qmmminputgenerator.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmtopologypreprocessor.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmoptions.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmmforceprovider.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/qmmm.cpp.o" "CMakeFiles/qmmm_applied_forces-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/qmmm_applied_forces-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 63%] Built target qmmm_applied_forces-test /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -MF CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o.d -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -MF CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o.d -o CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestdata.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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colvars_applied_forces-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make 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cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nbnxm-test.dir/link.d "CMakeFiles/nbnxm-test.dir/exclusions.cpp.o" "CMakeFiles/nbnxm-test.dir/kernel_test.cpp.o" "CMakeFiles/nbnxm-test.dir/kernelsetup.cpp.o" "CMakeFiles/nbnxm-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/nbnxm-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 64%] Built target nbnxm-test /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/accessor_policy.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/fft-test.dir/link.d "CMakeFiles/fft-test.dir/fft.cpp.o" "CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 64%] Built target fft-test /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build.make src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/enerdata.cpp.o -MF 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask32.cpp.o -MF CMakeFiles/utility-test.dir/bitmask32.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask32.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a "CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o" "CMakeFiles/mdrunutility-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extents.cpp.o -MF CMakeFiles/mdspan-test.dir/extents.cpp.o.d -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/extents.cpp [ 64%] Built target mdrunutility-test-shared /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -MF CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o.d -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -MF CMakeFiles/math-test.dir/coordinatetransformation.cpp.o.d -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/coordinatetransformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -MF CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o.d -o CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/observablesreducer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/listed_forces-test.dir/link.d "CMakeFiles/listed_forces-test.dir/bonded.cpp.o" "CMakeFiles/listed_forces-test.dir/pairs.cpp.o" "CMakeFiles/listed_forces-test.dir/position_restraints.cpp.o" "CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target listed_forces-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/extensions.cpp.o -MF CMakeFiles/mdspan-test.dir/extensions.cpp.o.d -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/tests/extensions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/bitmask64.cpp.o -MF CMakeFiles/utility-test.dir/bitmask64.cpp.o.d -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/bitmask64.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 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-DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include 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cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -MF CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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--verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/onlinehelp-test.dir/link.d "CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o" "CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o" "CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -MF CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/gpueventsynchronizer.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/hardware-test.dir/link.d "CMakeFiles/hardware-test.dir/cpuinfo.cpp.o" "CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/mockhardwaretopology.cpp.o" "CMakeFiles/hardware-test.dir/device_management.cpp.o" "CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target hardware-test /usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/cstringutil.cpp.o -MF CMakeFiles/utility-test.dir/cstringutil.cpp.o.d -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/cstringutil.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/awh-test.dir/link.d "CMakeFiles/awh-test.dir/awh_setup.cpp.o" "CMakeFiles/awh-test.dir/bias.cpp.o" "CMakeFiles/awh-test.dir/biasgrid.cpp.o" "CMakeFiles/awh-test.dir/biassharing.cpp.o" "CMakeFiles/awh-test.dir/biasstate.cpp.o" "CMakeFiles/awh-test.dir/bias_fep_lambda_state.cpp.o" "CMakeFiles/awh-test.dir/friction_metric.cpp.o" "CMakeFiles/awh-test.dir/__/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../../bin/awh-test ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 66%] Built target awh-test /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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'/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/typecasts.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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-Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -MF CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o.d -o CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestrunners_gpu.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -MF CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o.d -o CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/mdgpugraph.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -MF CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o.d -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/defaultinitializationallocator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -MF CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o.d -o CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settletestrunners_gpu.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gpu_utils-test.dir/link.d "CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_availability.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_stream_manager.cpp.o" "CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o" "CMakeFiles/gpu_utils-test.dir/pinnedmemorychecker.cpp.o" "CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o" "CMakeFiles/gpu_utils-test.dir/device_buffer.cpp.o" "CMakeFiles/gpu_utils-test.dir/gpueventsynchronizer.cpp.o" "CMakeFiles/gpu_utils-test.dir/typecasts.cpp.o" "CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 67%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/dofit.cpp.o -MF CMakeFiles/math-test.dir/dofit.cpp.o.d -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/dofit.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tables/tests/CMakeFiles/table-test.dir/splinetable.cpp.o -MF CMakeFiles/table-test.dir/splinetable.cpp.o.d -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/tests/splinetable.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/gammadistribution.cpp.o -MF CMakeFiles/random-test.dir/gammadistribution.cpp.o.d -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/gammadistribution.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/random/tests/CMakeFiles/random-test.dir/normaldistribution.cpp.o -MF CMakeFiles/random-test.dir/normaldistribution.cpp.o.d -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/random/tests/normaldistribution.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/restraintpotential-test.dir/link.d "CMakeFiles/restraintpotential-test.dir/manager.cpp.o" "CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 67%] Built target restraintpotential-test /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -MF CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o.d -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/exponentialmovingaverage.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/functions.cpp.o -MF CMakeFiles/math-test.dir/functions.cpp.o.d -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/functions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -MF CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o.d -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -MF CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o.d -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/fixedcapacityvector.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdlib-test.dir/link.d "CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o" "CMakeFiles/mdlib-test.dir/calcvir.cpp.o" "CMakeFiles/mdlib-test.dir/constr.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/ebin.cpp.o" "CMakeFiles/mdlib-test.dir/energydrifttracker.cpp.o" "CMakeFiles/mdlib-test.dir/energyoutput.cpp.o" "CMakeFiles/mdlib-test.dir/expanded.cpp.o" "CMakeFiles/mdlib-test.dir/freeenergyparameters.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrog.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/parrinellorahman.cpp.o" "CMakeFiles/mdlib-test.dir/settle.cpp.o" "CMakeFiles/mdlib-test.dir/settletestdata.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o" "CMakeFiles/mdlib-test.dir/shake.cpp.o" "CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o" "CMakeFiles/mdlib-test.dir/updategroups.cpp.o" "CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o" "CMakeFiles/mdlib-test.dir/constrtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/leapfrogtestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/mdgpugraph.cpp.o" "CMakeFiles/mdlib-test.dir/settletestrunners_gpu.cpp.o" "CMakeFiles/mdlib-test.dir/wholemoleculetransform.cpp.o" "CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 68%] Built target mdlib-test /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests/CMakeFiles/timing-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build.make src/gromacs/timing/tests/CMakeFiles/timing-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/timing/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/timing/tests/CMakeFiles/timing-test.dir/timing.cpp.o -MF CMakeFiles/timing-test.dir/timing.cpp.o.d -o CMakeFiles/timing-test.dir/timing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests/timing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/mshift.cpp.o -MF CMakeFiles/pbcutil-test.dir/mshift.cpp.o.d -o CMakeFiles/pbcutil-test.dir/mshift.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/mshift.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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&& /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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src/gromacs/math/tests/CMakeFiles/math-test.dir/densityfittingforce.cpp.o -MF CMakeFiles/math-test.dir/densityfittingforce.cpp.o.d -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/densityfittingforce.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/taskassignment-test.dir/link.d "CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o" "CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o ../CMakeFiles/taskassignment.dir/decidesimulationworkload.cpp.o ../CMakeFiles/taskassignment.dir/findallgputasks.cpp.o ../CMakeFiles/taskassignment.dir/reportgpuusage.cpp.o 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/pbc.cpp.o -MF CMakeFiles/pbcutil-test.dir/pbc.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/pbc.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" 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/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_DYNAMIC_REGISTRATION=true -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o.d -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/pbcenums.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/matrix.cpp.o -MF CMakeFiles/math-test.dir/matrix.cpp.o.d -o CMakeFiles/math-test.dir/matrix.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/matrix.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -MF CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o.d -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/ewald-test.dir/link.d "CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o" "CMakeFiles/ewald-test.dir/pmegathertest.cpp.o" "CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o" "CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o" "CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o" "CMakeFiles/ewald-test.dir/pme.cpp.o" "CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -lmuparser /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 70%] Built target ewald-test /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pbcutil-test.dir/link.d "CMakeFiles/pbcutil-test.dir/com.cpp.o" "CMakeFiles/pbcutil-test.dir/mshift.cpp.o" "CMakeFiles/pbcutil-test.dir/pbc.cpp.o" "CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o" "CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/table-test.dir/link.d "CMakeFiles/table-test.dir/splinetable.cpp.o" "CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 70%] Built target pbcutil-test /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake "--color=" [ 70%] Built target table-test /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/compat/tests/CMakeFiles/compat-test.dir/mp11.cpp.o -MF CMakeFiles/compat-test.dir/mp11.cpp.o.d -o CMakeFiles/compat-test.dir/mp11.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/tests/mp11.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -MF CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o.d -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -MF CMakeFiles/topology-test.dir/exclusionblocks.cpp.o.d -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/exclusionblocks.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/random-test.dir/link.d "CMakeFiles/random-test.dir/exponentialdistribution.cpp.o" "CMakeFiles/random-test.dir/gammadistribution.cpp.o" "CMakeFiles/random-test.dir/normaldistribution.cpp.o" "CMakeFiles/random-test.dir/seed.cpp.o" "CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o" "CMakeFiles/random-test.dir/threefry.cpp.o" "CMakeFiles/random-test.dir/uniformintdistribution.cpp.o" "CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o" "CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pull-test.dir/link.d "CMakeFiles/pull-test.dir/pull.cpp.o" "CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../CMakeFiles/pulling.dir/output.cpp.o ../CMakeFiles/pulling.dir/pull.cpp.o ../CMakeFiles/pulling.dir/pull_rotation.cpp.o ../CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o ../CMakeFiles/pulling.dir/pullutil.cpp.o ../CMakeFiles/pulling.dir/transformationcoordinate.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lmuparser -lm ../../../../lib/libgtest.so.1.13.0 /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a /usr/lib/aarch64-linux-gnu/libmuparser.so.2.3.4 [ 71%] Built target random-test make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake "--color=" [ 72%] Built target pull-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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'/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/vectypes.cpp.o -MF CMakeFiles/math-test.dir/vectypes.cpp.o.d -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/vectypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/listoflists.cpp.o -MF CMakeFiles/utility-test.dir/listoflists.cpp.o.d -o CMakeFiles/utility-test.dir/listoflists.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/listoflists.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/idef.cpp.o -MF CMakeFiles/topology-test.dir/idef.cpp.o.d -o CMakeFiles/topology-test.dir/idef.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/idef.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/math/tests/CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdtypes/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdtypes/tests/CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_mindist.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/compat-test.dir/link.d "CMakeFiles/compat-test.dir/mp11.cpp.o" "CMakeFiles/compat-test.dir/pointers.cpp.o" "CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 74%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/optionsassigner.cpp.o -MF CMakeFiles/options-test.dir/optionsassigner.cpp.o.d -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/tests/optionsassigner.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdtypes-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdtypes-test.dir/link.d "CMakeFiles/mdtypes-test.dir/enerdata.cpp.o" "CMakeFiles/mdtypes-test.dir/observablesreducer.cpp.o" "CMakeFiles/mdtypes-test.dir/checkpointdata.cpp.o" "CMakeFiles/mdtypes-test.dir/forcebuffers.cpp.o" "CMakeFiles/mdtypes-test.dir/multipletimestepping.cpp.o" "CMakeFiles/mdtypes-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/mdtypes-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 75%] Built target mdtypes-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genion.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/index.cpp.o -MF CMakeFiles/topology-test.dir/index.cpp.o.d -o CMakeFiles/topology-test.dir/index.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -MF CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o.d -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_util.cpp.o -MF CMakeFiles/simd-test.dir/scalar_util.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar_util.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/genrestr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gen_maxwell_velocities.cpp.o -MF 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -MF CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o.d -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pdb2gmx1-test.dir/link.d "CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp [ 75%] Built target pdb2gmx1-test /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/autocorr.cpp.o -MF CMakeFiles/correlations-test.dir/autocorr.cpp.o.d -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/logger.cpp.o -MF CMakeFiles/utility-test.dir/logger.cpp.o.d -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/logger.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/scalar_math.cpp.o -MF CMakeFiles/simd-test.dir/scalar_math.cpp.o.d -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/scalar_math.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxana-test.dir/link.d "CMakeFiles/gmxana-test.dir/entropy.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_chi.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o" "CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o" "CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 76%] Built target gmxana-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/datatest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include 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/usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/expfit.cpp.o -MF CMakeFiles/correlations-test.dir/expfit.cpp.o.d -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/pdb2gmx3-test.dir/link.d "CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o" "CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 76%] Built target pdb2gmx3-test /usr/bin/make -f 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directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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"CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/grompp_directives.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/massrepartitioning.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o" "CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 76%] Built target gmxpreprocess-test /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/topsort.cpp.o -MF CMakeFiles/topology-test.dir/topsort.cpp.o.d -o CMakeFiles/topology-test.dir/topsort.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/topsort.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/correlations-test.dir/link.d "CMakeFiles/correlations-test.dir/autocorr.cpp.o" "CMakeFiles/correlations-test.dir/correlationdataset.cpp.o" "CMakeFiles/correlations-test.dir/expfit.cpp.o" "CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o" "CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 76%] Built target correlations-test /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/energyanalysis-test.dir/link.d "CMakeFiles/energyanalysis-test.dir/energyterm.cpp.o" "CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o" "CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a 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src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/checkpoint.cpp.o -MF CMakeFiles/fileio-test.dir/checkpoint.cpp.o.d -o CMakeFiles/fileio-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/checkpoint.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/strconvert.cpp.o -MF CMakeFiles/utility-test.dir/strconvert.cpp.o.d -o CMakeFiles/utility-test.dir/strconvert.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/strconvert.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_memory.cpp.o -MF CMakeFiles/simd-test.dir/simd_memory.cpp.o.d -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_memory.cpp /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp: In static member function 'static std::vector > gmx::test::SimdMathTest::generateTestPoints(Range, std::size_t)': /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_math.cpp:169:19: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 169 | std::vector SimdMathTest::generateTestPoints(Range inputRange, std::size_t inputPoints) | ^~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/topology/tests/CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/report_methods.cpp.o -MF CMakeFiles/tool-test.dir/report_methods.cpp.o.d -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/report_methods.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -MF CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o.d -o CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/stringtoenumvalueconverter.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -MF CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o.d -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd_vector_operations.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/topology-test.dir/link.d "CMakeFiles/topology-test.dir/atoms.cpp.o" "CMakeFiles/topology-test.dir/exclusionblocks.cpp.o" "CMakeFiles/topology-test.dir/idef.cpp.o" "CMakeFiles/topology-test.dir/index.cpp.o" "CMakeFiles/topology-test.dir/mtop.cpp.o" "CMakeFiles/topology-test.dir/symtab.cpp.o" "CMakeFiles/topology-test.dir/topsort.cpp.o" "CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 77%] Built target topology-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -MF CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/nbsearch.cpp.o -MF CMakeFiles/selection-test.dir/nbsearch.cpp.o.d -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/nbsearch.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/simd/tests/CMakeFiles/simd-test.dir/simd4.cpp.o -MF CMakeFiles/simd-test.dir/simd4.cpp.o.d -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/tests/simd4.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/trjconv.cpp.o -MF CMakeFiles/tool-test.dir/trjconv.cpp.o.d -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/trjconv.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 79%] Built target math-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/densityfittingmodule.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a "CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o" "CMakeFiles/analysisdata-test-shared.dir/__/__/__/testutils/unittest_main.cpp.o" /usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 80%] Built target analysisdata-test-shared /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -MF CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/checkpoint.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -MF CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/helpwriting.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectioncollection.cpp.o -MF CMakeFiles/selection-test.dir/selectioncollection.cpp.o.d -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/selectioncollection.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/selectionoption.cpp.o -MF CMakeFiles/selection-test.dir/selectionoption.cpp.o.d -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/selectionoption.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/simd-test.dir/link.d "CMakeFiles/simd-test.dir/base.cpp.o" "CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o" "CMakeFiles/simd-test.dir/scalar.cpp.o" "CMakeFiles/simd-test.dir/scalar_util.cpp.o" "CMakeFiles/simd-test.dir/scalar_math.cpp.o" "CMakeFiles/simd-test.dir/simd.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o" "CMakeFiles/simd-test.dir/simd_integer.cpp.o" "CMakeFiles/simd-test.dir/simd_math.cpp.o" "CMakeFiles/simd-test.dir/simd_memory.cpp.o" "CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/simd4.cpp.o" "CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o" "CMakeFiles/simd-test.dir/simd4_math.cpp.o" "CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o" "CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 81%] Built target simd-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY 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-O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -MF CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o.d -o CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multiple_time_stepping.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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-O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/register.cpp.o -MF CMakeFiles/coordinateio-test.dir/register.cpp.o.d -o CMakeFiles/coordinateio-test.dir/register.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/register.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/convert-tpr.cpp.o -MF CMakeFiles/tool-test.dir/convert-tpr.cpp.o.d -o CMakeFiles/tool-test.dir/convert-tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/convert-tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/mimic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/toputils.cpp.o -MF CMakeFiles/selection-test.dir/toputils.cpp.o.d -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -MF CMakeFiles/fileio-test.dir/mrcserializer.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/mrcserializer.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/options/tests/CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -MF CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o.d -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/requirements.cpp.o -MF CMakeFiles/coordinateio-test.dir/requirements.cpp.o.d -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/requirements.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/selection/tests/CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/options-test.dir/link.d "CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o" "CMakeFiles/options-test.dir/filenameoption.cpp.o" "CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o" "CMakeFiles/options-test.dir/option.cpp.o" "CMakeFiles/options-test.dir/optionsassigner.cpp.o" "CMakeFiles/options-test.dir/repeatingsection.cpp.o" "CMakeFiles/options-test.dir/timeunitmanager.cpp.o" "CMakeFiles/options-test.dir/treesupport.cpp.o" "CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 83%] Built target options-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/dispersion_correction.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/tools/tests/CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/ewaldsurfaceterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/template_mp.cpp.o -MF CMakeFiles/utility-test.dir/template_mp.cpp.o.d -o CMakeFiles/utility-test.dir/template_mp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/mrcdensitymap.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-modules-test.dir/link.d "CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o" "CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o" "CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o" "CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 83%] Built target mdrun-modules-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" 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-DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/tool-test.dir/link.d "CMakeFiles/tool-test.dir/dump.cpp.o" "CMakeFiles/tool-test.dir/helpwriting.cpp.o" "CMakeFiles/tool-test.dir/make_ndx.cpp.o" "CMakeFiles/tool-test.dir/report_methods.cpp.o" "CMakeFiles/tool-test.dir/trjconv.cpp.o" "CMakeFiles/tool-test.dir/convert-tpr.cpp.o" "CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 83%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -MF 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src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -MF CMakeFiles/coordinateio-test.dir/setatoms.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/setatoms.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/gromacs/utility/tests/CMakeFiles/utility-test.dir/textreader.cpp.o -MF CMakeFiles/utility-test.dir/textreader.cpp.o.d -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/textreader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -MF CMakeFiles/mdrun-test.dir/swapcoords.cpp.o.d -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/swapcoords.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-output-test.dir/link.d "CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o" "CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o" "CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o" "CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o" "CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 84%] Built target mdrun-output-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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-DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -MF CMakeFiles/mdrun-test.dir/freezegroups.cpp.o.d -o CMakeFiles/mdrun-test.dir/freezegroups.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freezegroups.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -MF CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o.d -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/mrcdensitymapheader.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -MF CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o.d -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/tests/setbothtime.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -MF CMakeFiles/mdrun-io-test.dir/grompp.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/grompp.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-single-rank-algorithms-test.dir/link.d "CMakeFiles/mdrun-single-rank-algorithms-test.dir/dispersion_correction.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/ewaldsurfaceterm.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/orires.cpp.o" "CMakeFiles/mdrun-single-rank-algorithms-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-single-rank-algorithms-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 84%] Built target mdrun-single-rank-algorithms-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -MF CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o.d -o CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/constantacceleration.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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'/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -MF CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/initialconstraints.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-tpi-test.dir/link.d "CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o" "CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 84%] Built target mdrun-tpi-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/readinp.cpp.o -MF CMakeFiles/fileio-test.dir/readinp.cpp.o.d -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/readinp.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/minimize-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/selection-test.dir/link.d "CMakeFiles/selection-test.dir/indexutil.cpp.o" "CMakeFiles/selection-test.dir/nbsearch.cpp.o" "CMakeFiles/selection-test.dir/poscalc.cpp.o" "CMakeFiles/selection-test.dir/selectioncollection.cpp.o" "CMakeFiles/selection-test.dir/selectionoption.cpp.o" "CMakeFiles/selection-test.dir/toputils.cpp.o" "CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 85%] Built target selection-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/multisimtest.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/minimize-test.dir/link.d "CMakeFiles/minimize-test.dir/minimize.cpp.o" "CMakeFiles/minimize-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/minimize-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 85%] Built target minimize-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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/build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o -MF CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o.d -o 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -MF CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o.d -o CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange_equivalence.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/termination.cpp.o -MF CMakeFiles/mdrun-io-test.dir/termination.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/termination.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/utility/tests/CMakeFiles/utility-test.dir/typetraits.cpp.o -MF CMakeFiles/utility-test.dir/typetraits.cpp.o.d -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/typetraits.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -MF CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o.d -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simple_mdrun.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/tngio.cpp.o -MF CMakeFiles/fileio-test.dir/tngio.cpp.o.d -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/tngio.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/coordinateio-test.dir/link.d "CMakeFiles/coordinateio-test.dir/builder.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o" "CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o" "CMakeFiles/coordinateio-test.dir/register.cpp.o" "CMakeFiles/coordinateio-test.dir/requirements.cpp.o" "CMakeFiles/coordinateio-test.dir/setatoms.cpp.o" "CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o" "CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o" "CMakeFiles/coordinateio-test.dir/settimestep.cpp.o" "CMakeFiles/coordinateio-test.dir/testmodule.cpp.o" "CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 85%] Built target coordinateio-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-basic-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem 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src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_coupling.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-pme-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-mpi-pme-test.dir/link.d "CMakeFiles/mdrun-mpi-pme-test.dir/pmetest.cpp.o" "CMakeFiles/mdrun-mpi-pme-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-pme-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 87%] Built target mdrun-mpi-pme-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-constraints-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd 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/usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-test.dir/link.d "CMakeFiles/mdrun-multisim-test.dir/multisim.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 87%] Built target mdrun-multisim-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -MF CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o.d -o CMakeFiles/mdrun-fep-test.dir/freeenergy.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/utility-test.dir/link.d "CMakeFiles/utility-test.dir/alignedallocator.cpp.o" "CMakeFiles/utility-test.dir/arrayref.cpp.o" "CMakeFiles/utility-test.dir/booltype.cpp.o" "CMakeFiles/utility-test.dir/bitmask32.cpp.o" "CMakeFiles/utility-test.dir/bitmask64.cpp.o" "CMakeFiles/utility-test.dir/bitmask128.cpp.o" "CMakeFiles/utility-test.dir/cstringutil.cpp.o" "CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o" "CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o" "CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o" "CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o" "CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o" "CMakeFiles/utility-test.dir/listoflists.cpp.o" "CMakeFiles/utility-test.dir/logger.cpp.o" "CMakeFiles/utility-test.dir/message_string_collector.cpp.o" "CMakeFiles/utility-test.dir/path.cpp.o" "CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o" "CMakeFiles/utility-test.dir/range.cpp.o" "CMakeFiles/utility-test.dir/strconvert.cpp.o" "CMakeFiles/utility-test.dir/stringtoenumvalueconverter.cpp.o" "CMakeFiles/utility-test.dir/stringutil.cpp.o" "CMakeFiles/utility-test.dir/template_mp.cpp.o" "CMakeFiles/utility-test.dir/textreader.cpp.o" "CMakeFiles/utility-test.dir/textwriter.cpp.o" "CMakeFiles/utility-test.dir/typetraits.cpp.o" "CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 ../../../../lib/libgmock.so.1.13.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 88%] Built target utility-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/pull.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/pull.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-test.dir/link.d "CMakeFiles/mdrun-test.dir/multiple_time_stepping.cpp.o" "CMakeFiles/mdrun-test.dir/swapcoords.cpp.o" "CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o" "CMakeFiles/mdrun-test.dir/freezegroups.cpp.o" "CMakeFiles/mdrun-test.dir/constantacceleration.cpp.o" "CMakeFiles/mdrun-test.dir/boxdeformation.cpp.o" "CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 89%] Built target mdrun-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -MF CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o.d -o CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/replicaexchange.cpp.o" "CMakeFiles/mdrun-multisim-replex-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 89%] Built target mdrun-multisim-replex-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -MF CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o.d -o CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-io-test.dir/link.d "CMakeFiles/mdrun-io-test.dir/checkpoint.cpp.o" "CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o" "CMakeFiles/mdrun-io-test.dir/grompp.cpp.o" "CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o" "CMakeFiles/mdrun-io-test.dir/termination.cpp.o" "CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 89%] Built target mdrun-io-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-non-integrator-test.dir/link.d "CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o" "CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 89%] Built target mdrun-non-integrator-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem 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/build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/periodicactions_basic.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-coordination-coupling-test.dir/link.d "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/periodicactions_coupling.cpp.o" "CMakeFiles/mdrun-coordination-coupling-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-coordination-coupling-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 89%] Built target mdrun-coordination-coupling-test /usr/bin/make -f api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd 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../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 90%] Built target fileio-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f 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api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-fep-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/link.d "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/multisimtest.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/replicaexchange_equivalence.cpp.o" "CMakeFiles/mdrun-multisim-replex-equivalence-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-multisim-replex-equivalence-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 90%] Built target mdrun-multisim-replex-equivalence-test /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make api/gmxapi/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include 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../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-fep-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 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-DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-simulator-comparison-test.dir/link.d "CMakeFiles/mdrun-simulator-comparison-test.dir/simulator.cpp.o" "CMakeFiles/mdrun-simulator-comparison-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-simulator-comparison-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 92%] Built target mdrun-simulator-comparison-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/CMakeFiles/nblib-setup-test.dir/DependInfo.cmake "--color=" /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-rotation-test.dir/link.d "CMakeFiles/mdrun-rotation-test.dir/pull_rotation.cpp.o" "CMakeFiles/mdrun-rotation-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-rotation-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-setup-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/box.cpp.o -MF CMakeFiles/nblib-setup-test.dir/box.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/box.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/box.cpp [ 92%] Built target mdrun-rotation-test /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/tpr.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/tpr.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-basic-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/CMakeFiles/nblib-integration-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build.make api/nblib/tests/CMakeFiles/nblib-integration-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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/build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -MF CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/nbkernelsystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-vsites-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/workflow-details-test.dir/link.d "CMakeFiles/workflow-details-test.dir/workflow.cpp.o" "CMakeFiles/workflow-details-test.dir/__/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../../lib/libgmock.so.1.13.0 ../../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target workflow-details-test /usr/bin/make -f api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/build.make api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests /build/reproducible-path/gromacs-2024.4/build/mpi 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/bondtypes.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/mdrun-vsites-test.dir/link.d "CMakeFiles/mdrun-vsites-test.dir/virtualsites.cpp.o" "CMakeFiles/mdrun-vsites-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-vsites-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target mdrun-vsites-test /usr/bin/make -f api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/build.make api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests 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/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-coordination-constraints-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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93%] Built target workflow-details-mpi-test /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem 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../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target mdrun-coordination-constraints-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/mpi 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -MF CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/mdmodulesnotifier.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/mdmodulesnotifier.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/programs/mdrun/tests/CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrun-pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/gmxcalculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/util/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/util/tests/CMakeFiles/nblib-util-test.dir/traits.cpp.o -MF CMakeFiles/nblib-util-test.dir/traits.cpp.o.d -o CMakeFiles/nblib-util-test.dir/traits.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/util/tests/traits.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include 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api/nblib/tests/CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-tpr-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-pull-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -MF CMakeFiles/nblib-integration-test.dir/simstate.cpp.o.d -o CMakeFiles/nblib-integration-test.dir/simstate.cpp.o -c 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'/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target mdrun-pull-test /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -MF CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o.d -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-tpr-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem 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make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target nblib-tpr-test /usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f 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/usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -MF CMakeFiles/nblib-setup-test.dir/particletype.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/particletype.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/tests/particletype.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include 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-ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/listedtesthelpers.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-util-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-util-test.dir/link.d "CMakeFiles/nblib-util-test.dir/setup.cpp.o" "CMakeFiles/nblib-util-test.dir/traits.cpp.o" "CMakeFiles/nblib-util-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-util-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target nblib-util-test /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem 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-DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/status.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integrator-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-integration-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integrator-test.dir/link.d "CMakeFiles/nblib-integrator-test.dir/integrator.cpp.o" "CMakeFiles/nblib-integrator-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integrator-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 93%] Built target nblib-integrator-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/stopsignaler.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-integration-test.dir/link.d "CMakeFiles/nblib-integration-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-integration-test.dir/nbkernelsystem.cpp.o" "CMakeFiles/nblib-integration-test.dir/simstate.cpp.o" "CMakeFiles/nblib-integration-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-integration-test ../../../lib/libtestutils.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 94%] Built target nblib-integration-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -MF CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o.d -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/system.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG 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-I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF 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-I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/tests/CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -MF CMakeFiles/nblib-setup-test.dir/molecules.cpp.o.d -o CMakeFiles/nblib-setup-test.dir/molecules.cpp.o -c 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/build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/version.cpp.o -MF CMakeFiles/gmxapi-test.dir/version.cpp.o.d -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests/version.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/typetests.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi-mpi-test.dir/link.d "CMakeFiles/gmxapi-mpi-test.dir/context.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-mpi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 96%] Built target gmxapi-mpi-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/calculator.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -MF CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o.d -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/gmxapi/cpp/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/tests -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/gmxapi/cpp/tests/CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops 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-I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/nblib/listed_forces/tests/conversions.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -MF CMakeFiles/analysisdata-test.dir/arraydata.cpp.o.d -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/gmxapi-test.dir/link.d "CMakeFiles/gmxapi-test.dir/restraint.cpp.o" "CMakeFiles/gmxapi-test.dir/runner.cpp.o" "CMakeFiles/gmxapi-test.dir/status.cpp.o" "CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o" "CMakeFiles/gmxapi-test.dir/system.cpp.o" "CMakeFiles/gmxapi-test.dir/version.cpp.o" "CMakeFiles/gmxapi-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_mpi.so.0.4.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 96%] Built target gmxapi-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g 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-I/build/reproducible-path/gromacs-2024.4/api -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem 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CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/scattering.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"api/nblib/listed_forces/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/api/nblib/tests -I/build/reproducible-path/gromacs-2024.4/api/nblib/include -I/build/reproducible-path/gromacs-2024.4/api/nblib -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT api/nblib/listed_forces/tests/CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -MF CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o.d -o CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/analysisdata-test.dir/link.d "CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o" "CMakeFiles/analysisdata-test.dir/arraydata.cpp.o" "CMakeFiles/analysisdata-test.dir/average.cpp.o" "CMakeFiles/analysisdata-test.dir/histogram.cpp.o" "CMakeFiles/analysisdata-test.dir/lifetime.cpp.o" "CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 96%] Built target analysisdata-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/commandline-test.dir/link.d "CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o" "CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o" "CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o" "CMakeFiles/commandline-test.dir/filenm.cpp.o" "CMakeFiles/commandline-test.dir/pargs.cpp.o" "CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o" -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/mpicxx -DGMX_DOUBLE=0 -DGTEST_LANG_CXX11 -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/testutils/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/mpi/api/legacy/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googlemock -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++17 -fexcess-precision=fast -funroll-all-loops -Wno-missing-field-initializers -fopenmp -MD -MT src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -MF CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o.d -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/testutils/unittest_main.cpp [ 96%] Built target commandline-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-setup-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-setup-test.dir/link.d "CMakeFiles/nblib-setup-test.dir/box.cpp.o" "CMakeFiles/nblib-setup-test.dir/interactions.cpp.o" "CMakeFiles/nblib-setup-test.dir/particletype.cpp.o" "CMakeFiles/nblib-setup-test.dir/pbcholder.cpp.o" "CMakeFiles/nblib-setup-test.dir/molecules.cpp.o" "CMakeFiles/nblib-setup-test.dir/nbnxmsetup.cpp.o" "CMakeFiles/nblib-setup-test.dir/topology.cpp.o" "CMakeFiles/nblib-setup-test.dir/virials.cpp.o" "CMakeFiles/nblib-setup-test.dir/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../bin/nblib-setup-test ../../../lib/libtestutils.a ../../../lib/libmdrun_test_infrastructure.a ../../../lib/libnblib_test_infrastructure.a ../../../lib/libnblib_gmx.so.0.1.0 ../../../lib/libtestutils.a ../../../lib/libgmock.so.1.13.0 ../../../lib/libgtest.so.1.13.0 ../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target nblib-setup-test /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/CMakeFiles/nblib-tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib-tests.dir/build.make api/nblib/CMakeFiles/nblib-tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'api/nblib/CMakeFiles/nblib-tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target nblib-tests cd /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/nblib-listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/nblib-listed-forces-test.dir/link.d "CMakeFiles/nblib-listed-forces-test.dir/bondtypes.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/gmxcalculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/helpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/listedtesthelpers.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/kernels.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/typetests.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/calculator.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/conversions.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/shiftforces.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/transformations.cpp.o" "CMakeFiles/nblib-listed-forces-test.dir/__/__/__/__/src/testutils/unittest_main.cpp.o" -o ../../../../bin/nblib-listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libnblib_test_infrastructure.a ../../../../lib/libnblib_gmx.so.0.1.0 ../../../../lib/libtestutils.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 97%] Built target nblib-listed-forces-test cd /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1 /usr/bin/mpicxx -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/trajectoryanalysis-test.dir/link.d "CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/dssp.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/gyrate.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/hbond.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/msd.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/scattering.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o" "CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o" ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mpi.so.9.0.0 -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a ../../../../lib/libgmock.so.1.13.0 ../../../../lib/libgtest.so.1.13.0 make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target trajectoryanalysis-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/tests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target tests make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' (cd build/mpi ; LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/mpi/lib \ OMPI_MCA_rmaps_base_oversubscribe=1 \ PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe \ ctest -V) UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/mpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gromacs-2024.4/build/mpi/DartConfiguration.tcl Parse Config file:/build/reproducible-path/gromacs-2024.4/build/mpi/DartConfiguration.tcl Test project /build/reproducible-path/gromacs-2024.4/build/mpi Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: GmxapiExternalInterfaceTests 1: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxapiExternalInterfaceTests.xml" 1: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests 1: Test timeout computed to be: 600 1: [==========] Running 9 tests from 1 test suite. 1: [----------] Global test environment set-up. 1: [----------] 9 tests from GmxApiTest 1: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -29528354 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.084 0.042 199.7 1: (ns/day) (hour/ns) 1: Performance: 12.056 1.991 1: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (791 ms) 1: [ RUN ] GmxApiTest.RunnerBasicMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1613766725 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 23 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.093 0.047 199.6 1: (ns/day) (hour/ns) 1: Performance: 10.851 2.212 1: [ OK ] GmxApiTest.RunnerBasicMD (526 ms) 1: [ RUN ] GmxApiTest.RunnerReinitialize 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: 1: Received the remote INT/TERM signal, stopping within 200 steps 1: 1: Setting the LD random seed to -1394192915 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.547 0.273 199.9 1: (ns/day) (hour/ns) 1: Performance: 12.964 1.851 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 20 steps, 0.0 ps. 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.596 0.298 200.0 1: (ns/day) (hour/ns) 1: Performance: 11.890 2.018 1: [ OK ] GmxApiTest.RunnerReinitialize (1016 ms) 1: [ RUN ] GmxApiTest.RunnerChainedMD 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 2 steps, 0.0 ps. 1: Setting the LD random seed to -1135146 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.189 0.094 199.8 1: (ns/day) (hour/ns) 1: Performance: 5.358 4.479 1: trr version: GMX_trn_file (single precision) 1: 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Setting nsteps to 4 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 1: Input file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 2 1: Runtime for the run 0.00390625 ps 1: Run end step 2 1: Run end time 0.00390625 ps 1: 1: 1: Output file: 1: Run start step 0 1: Run start time 0 ps 1: Step to be made during run 4 1: Runtime for the run 0.0078125 ps 1: Run end step 4 1: Run end time 0.0078125 ps 1: 1: 1: Writing final coordinates. 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.165 0.083 199.8 1: (ns/day) (hour/ns) 1: Performance: 6.127 3.917 1: 1: [ OK ] GmxApiTest.RunnerChainedMD (1207 ms) 1: [ RUN ] GmxApiTest.Status 1: [ OK ] GmxApiTest.Status (0 ms) 1: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: Setting the LD random seed to -275330209 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: 1: Writing final coordinates. 1: 1: NOTE: 27 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.194 0.097 199.8 1: (ns/day) (hour/ns) 1: Performance: 8.707 2.756 1: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 1: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 1: Changing nstlist from 10 to 1, rlist from 1.057 to 1 1: 1: 1: Using 1 MPI process 1: Using 2 OpenMP threads 1: 1: 1: NOTE: The number of threads is not equal to the number of (logical) cpus 1: and the -pin option is set to auto: will not pin threads to cpus. 1: This can lead to significant performance degradation. 1: Consider using -pin on (and -pinoffset in case you run multiple jobs). 1: starting mdrun 'Water and methane' 1: 4 steps, 0.0 ps. 1: 1: NOTE: 13 % of the run time was spent in pair search, 1: you might want to increase nstlist (this has no effect on accuracy) 1: 1: Core t (s) Wall t (s) (%) 1: Time: 0.039 0.020 199.4 1: (ns/day) (hour/ns) 1: Performance: 17.141 1.400 1: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (1135 ms) 1: [ RUN ] GmxApiTest.SystemConstruction 1: Generating 1-4 interactions: fudge = 0.5 1: 1: NOTE 1 [file spc_and_methane.top, line 33]: 1: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 1: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 1: the time step of 2.0e-03 ps. 1: Maybe you forgot to change the constraints mdp option. 1: 1: Number of degrees of freedom in T-Coupling group System is 18.00 1: 1: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 1: You are using a plain Coulomb cut-off, which might produce artifacts. 1: You might want to consider using PME electrostatics. 1: 1: 1: 1: There were 2 NOTEs 1: Setting the LD random seed to -167772723 1: 1: Generated 331705 of the 331705 non-bonded parameter combinations 1: 1: Generated 331705 of the 331705 1-4 parameter combinations 1: 1: Excluding 2 bonded neighbours molecule type 'SOL' 1: 1: Excluding 3 bonded neighbours molecule type 'methane' 1: 1: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 1: 1: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 1: 1: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 1: 1: Note that mdrun will redetermine rlist based on the actual pair-list setup 1: 1: This run will generate roughly 0 Mb of data 1: [ OK ] GmxApiTest.SystemConstruction (888 ms) 1: [ RUN ] GmxApiTest.SaneVersionComparisons 1: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 1: [ RUN ] GmxApiTest.VersionNamed0_1_Features 1: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 1: [----------] 9 tests from GmxApiTest (5566 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 9 tests from 1 test suite ran. (5571 ms total) 1: [ PASSED ] 9 tests. 1/91 Test #1: GmxapiExternalInterfaceTests ................. Passed 5.78 sec test 2 Start 2: GmxapiMpiTests 2: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxapi-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxapiMpiTests.xml" 2: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests 2: Test timeout computed to be: 600 2: [==========] Running 13 tests from 1 test suite. 2: [----------] Global test environment set-up. 2: [----------] 13 tests from GmxApiTest 2: [ RUN ] GmxApiTest.AllContext 2: [ OK ] GmxApiTest.AllContext (183 ms) 2: [ RUN ] GmxApiTest.NullContext 2: [ OK ] GmxApiTest.NullContext (0 ms) 2: [ RUN ] GmxApiTest.MpiWorldContext 2: [ OK ] GmxApiTest.MpiWorldContext (167 ms) 2: [ RUN ] GmxApiTest.MpiSplitContext 2: [ OK ] GmxApiTest.MpiSplitContext (1069 ms) 2: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD 2: Setting the LD random seed to -643629207 2: Setting the LD random seed to -476110859 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 25 % of the run time was spent in domain decomposition, 2: 1 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 15 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 1.133 0.295 384.6 2: (ns/day) (hour/ns) 2: Performance: 1.719 13.962 2: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (3042 ms) 2: [ RUN ] GmxApiTest.RunnerBasicMD 2: Setting the LD random seed to 2058972143 2: Setting the LD random seed to -1050929 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 15 % of the run time was spent in domain decomposition, 2: 3 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 19 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.520 0.130 399.7 2: (ns/day) (hour/ns) 2: Performance: 3.891 6.168 2: [ OK ] GmxApiTest.RunnerBasicMD (3636 ms) 2: [ RUN ] GmxApiTest.RunnerReinitialize 2: Setting the LD random seed to 2113923003 2: Setting the LD random seed to -536973698 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: 2: Received the remote INT/TERM signal, stopping within 200 steps 2: 2: 2: Writing final coordinates. 2: 2: NOTE: 7 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 2.477 0.619 399.9 2: (ns/day) (hour/ns) 2: Performance: 5.722 4.194 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 20 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: Core t (s) Wall t (s) (%) 2: Time: 2.892 0.723 400.0 2: (ns/day) (hour/ns) 2: Performance: 4.900 4.898 2: [ OK ] GmxApiTest.RunnerReinitialize (2339 ms) 2: Setting the LD random seed to -17334545 2: [ RUN ] GmxApiTest.RunnerChainedMD 2: Setting the LD random seed to -205530377 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 2 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: NOTE: 20 % of the run time was spent in domain decomposition, 2: 4 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 11 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.514 0.141 366.0 2: (ns/day) (hour/ns) 2: Performance: 3.602 6.664 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Setting nsteps to 4 2: trr version: GMX_trn_file (single precision) 2: 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Setting nsteps to 4 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: Input file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 2 2: Runtime for the run 0.00390625 ps 2: Run end step 2 2: Run end time 0.00390625 ps 2: 2: 2: Output file: 2: Run start step 0 2: Run start time 0 ps 2: Step to be made during run 4 2: Runtime for the run 0.0078125 ps 2: Run end step 4 2: Run end time 0.0078125 ps 2: 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_RunnerChainedMD.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 25, rlist from 1.057 to 1.183 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 2: 2: Writing final coordinates. 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.352 0.088 399.7 2: (ns/day) (hour/ns) 2: Performance: 5.743 4.179 2: 2: 2: [ OK ] GmxApiTest.RunnerChainedMD (1199 ms) 2: [ RUN ] GmxApiTest.Status 2: [ OK ] GmxApiTest.Status (0 ms) 2: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient 2: Setting the LD random seed to 1329527647 2: Setting the LD random seed to -86008902 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: Writing final coordinates. 2: 2: 2: Dynamic load balancing report: 2: DLB was turned on during the run due to measured imbalance. 2: Average load imbalance: 56.0%. 2: The balanceable part of the MD step is 14%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 7.8%. 2: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 2: 2: NOTE: 7.8 % of the available CPU time was lost due to load imbalance 2: in the domain decomposition. 2: You can consider manually changing the decomposition (option -dd); 2: e.g. by using fewer domains along the box dimension in which there is 2: considerable inhomogeneity in the simulated system. 2: 2: NOTE: 40 % of the run time was spent in domain decomposition, 2: 11 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.819 0.205 399.8 2: (ns/day) (hour/ns) 2: Performance: 4.117 5.829 2: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 2: Overriding nsteps with value passed on the command line: 4 steps, 0.00781 ps 2: Changing nstlist from 10 to 1, rlist from 1.057 to 1 2: 2: 2: Using 2 MPI processes 2: Using 2 OpenMP threads per MPI process 2: 2: 2: NOTE: The number of threads is not equal to the number of (logical) cpus 2: and the -pin option is set to auto: will not pin threads to cpus. 2: This can lead to significant performance degradation. 2: Consider using -pin on (and -pinoffset in case you run multiple jobs). 2: starting mdrun 'Water and methane' 2: 4 steps, 0.0 ps. 2: 2: 2: Dynamic load balancing report: 2: DLB was off during the run due to low measured imbalance. 2: Average load imbalance: 50.3%. 2: The balanceable part of the MD step is 5%, load imbalance is computed from this. 2: Part of the total run time spent waiting due to load imbalance: 2.3%. 2: 2: 2: NOTE: 27 % of the run time was spent in domain decomposition, 2: 6 % of the run time was spent in pair search, 2: you might want to increase nstlist (this has no effect on accuracy) 2: 2: NOTE: 14 % of the run time was spent communicating energies, 2: you might want to increase some nst* mdp options 2: 2: Core t (s) Wall t (s) (%) 2: Time: 0.485 0.135 358.7 2: (ns/day) (hour/ns) 2: Performance: 2.499 9.605 2: Setting the LD random seed to -272781701 2: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (1172 ms) 2: [ RUN ] GmxApiTest.SystemConstruction 2: Setting the LD random seed to -537141576 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 non-bonded parameter combinations 2: Generating 1-4 interactions: fudge = 0.5 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: This run will generate roughly 0 Mb of data 2: 2: There were 2 NOTEs 2: 2: Generated 331705 of the 331705 1-4 parameter combinations 2: 2: Excluding 2 bonded neighbours molecule type 'SOL' 2: 2: Excluding 3 bonded neighbours molecule type 'methane' 2: 2: NOTE 1 [file spc_and_methane.top, line 33]: 2: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 2: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 2: the time step of 2.0e-03 ps. 2: Maybe you forgot to change the constraints mdp option. 2: 2: Number of degrees of freedom in T-Coupling group System is 18.00 2: 2: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]: 2: You are using a plain Coulomb cut-off, which might produce artifacts. 2: You might want to consider using PME electrostatics. 2: 2: 2: 2: There were 2 NOTEs 2: 2: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 2: 2: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 2: 2: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 2: 2: Note that mdrun will redetermine rlist based on the actual pair-list setup 2: 2: This run will generate roughly 0 Mb of data 2: [ OK ] GmxApiTest.SystemConstruction (680 ms) 2: [ RUN ] GmxApiTest.SaneVersionComparisons 2: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms) 2: [ RUN ] GmxApiTest.VersionNamed0_1_Features 2: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms) 2: [----------] 13 tests from GmxApiTest (13763 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 13 tests from 1 test suite ran. (13903 ms total) 2: [ PASSED ] 13 tests. 2/91 Test #2: GmxapiMpiTests ............................... Passed 15.88 sec test 3 Start 3: GmxapiInternalInterfaceTests 3: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxapiInternalInterfaceTests.xml" 3: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests 3: Test timeout computed to be: 600 3: [==========] Running 2 tests from 1 test suite. 3: [----------] Global test environment set-up. 3: [----------] 2 tests from GmxApiTest 3: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to 262020766 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.BuildApiWorkflowImpl (834 ms) 3: [ RUN ] GmxApiTest.CreateApiWorkflow 3: Generating 1-4 interactions: fudge = 0.5 3: 3: NOTE 1 [file spc_and_methane.top, line 33]: 3: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 3: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 3: the time step of 2.0e-03 ps. 3: Maybe you forgot to change the constraints mdp option. 3: 3: Number of degrees of freedom in T-Coupling group System is 18.00 3: 3: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 3: You are using a plain Coulomb cut-off, which might produce artifacts. 3: You might want to consider using PME electrostatics. 3: 3: 3: 3: There were 2 NOTEs 3: Setting the LD random seed to -84149258 3: 3: Generated 331705 of the 331705 non-bonded parameter combinations 3: 3: Generated 331705 of the 331705 1-4 parameter combinations 3: 3: Excluding 2 bonded neighbours molecule type 'SOL' 3: 3: Excluding 3 bonded neighbours molecule type 'methane' 3: 3: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 3: 3: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 3: 3: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 3: 3: Note that mdrun will redetermine rlist based on the actual pair-list setup 3: 3: This run will generate roughly 0 Mb of data 3: [ OK ] GmxApiTest.CreateApiWorkflow (561 ms) 3: [----------] 2 tests from GmxApiTest (1395 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 2 tests from 1 test suite ran. (1412 ms total) 3: [ PASSED ] 2 tests. 3/91 Test #3: GmxapiInternalInterfaceTests ................. Passed 1.72 sec test 4 Start 4: GmxapiInternalsMpiTests 4: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/workflow-details-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxapiInternalsMpiTests.xml" 4: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests 4: Test timeout computed to be: 600 4: [==========] Running 2 tests from 1 test suite. 4: [----------] Global test environment set-up. 4: [----------] 2 tests from GmxApiTest 4: Setting the LD random seed to -562183625 4: [ RUN ] GmxApiTest.BuildApiWorkflowImpl 4: Setting the LD random seed to -1074136386 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: This run will generate roughly 0 Mb of data 4: 4: There were 2 NOTEs 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: This run will generate roughly 0 Mb of data 4: Setting the LD random seed to -71438337 4: [ OK ] GmxApiTest.BuildApiWorkflowImpl (1003 ms) 4: [ RUN ] GmxApiTest.CreateApiWorkflow 4: Setting the LD random seed to -72089603 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 non-bonded parameter combinations 4: Generating 1-4 interactions: fudge = 0.5 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: This run will generate roughly 0 Mb of data 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: There were 2 NOTEs 4: 4: Generated 331705 of the 331705 1-4 parameter combinations 4: 4: Excluding 2 bonded neighbours molecule type 'SOL' 4: 4: Excluding 3 bonded neighbours molecule type 'methane' 4: 4: NOTE 1 [file spc_and_methane.top, line 33]: 4: The bond in molecule-type methane between atoms 1 C and 2 H1 has an 4: estimated oscillational period of 1.1e-02 ps, which is less than 10 times 4: the time step of 2.0e-03 ps. 4: Maybe you forgot to change the constraints mdp option. 4: 4: Number of degrees of freedom in T-Coupling group System is 18.00 4: 4: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 4: 4: Calculated rlist for 1x1 atom pair-list as 1.077 nm, buffer size 0.077 nm 4: 4: Set rlist, assuming 4x4 atom pair-list, to 1.057 nm, buffer size 0.057 nm 4: 4: Note that mdrun will redetermine rlist based on the actual pair-list setup 4: 4: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]: 4: You are using a plain Coulomb cut-off, which might produce artifacts. 4: You might want to consider using PME electrostatics. 4: 4: 4: 4: This run will generate roughly 0 Mb of data 4: 4: There were 2 NOTEs 4: [ OK ] GmxApiTest.CreateApiWorkflow (796 ms) 4: [----------] 2 tests from GmxApiTest (1848 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 2 tests from 1 test suite ran. (1967 ms total) 4: [ PASSED ] 2 tests. 4/91 Test #4: GmxapiInternalsMpiTests ...................... Passed 2.44 sec test 5 Start 5: NbLibListedForcesTests 5: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-listed-forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibListedForcesTests.xml" 5: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/listed_forces/tests 5: Test timeout computed to be: 600 5: [==========] Running 44 tests from 22 test suites. 5: [----------] Global test environment set-up. 5: [----------] 8 tests from NBlibTest 5: [ RUN ] NBlibTest.BondTypesOperatorEqualWorks 5: [ OK ] NBlibTest.BondTypesOperatorEqualWorks (0 ms) 5: [ RUN ] NBlibTest.BondTypesLessThanWorks 5: [ OK ] NBlibTest.BondTypesLessThanWorks (0 ms) 5: [ RUN ] NBlibTest.CanSplitListedWork 5: [ OK ] NBlibTest.CanSplitListedWork (0 ms) 5: [ RUN ] NBlibTest.ListedForceBuffer 5: [ OK ] NBlibTest.ListedForceBuffer (0 ms) 5: [ RUN ] NBlibTest.ListedForceCalculatorCanConstruct 5: [ OK ] NBlibTest.ListedForceCalculatorCanConstruct (0 ms) 5: [ RUN ] NBlibTest.GmxToNblibConversionAllTypes 5: [ OK ] NBlibTest.GmxToNblibConversionAllTypes (28 ms) 5: [ RUN ] NBlibTest.EndToEndListedComparison 5: [ OK ] NBlibTest.EndToEndListedComparison (0 ms) 5: [ RUN ] NBlibTest.shiftForcesAreCorrect 5: [ OK ] NBlibTest.shiftForcesAreCorrect (79 ms) 5: [----------] 8 tests from NBlibTest (109 ms total) 5: 5: [----------] 1 test from Kernels 5: [ RUN ] Kernels.HarmonicScalarKernelCanCompute 5: [ OK ] Kernels.HarmonicScalarKernelCanCompute (0 ms) 5: [----------] 1 test from Kernels (0 ms total) 5: 5: [----------] 1 test from FourCenter 5: [ RUN ] FourCenter.ListedForcesProperDihedralTest 5: [ OK ] FourCenter.ListedForcesProperDihedralTest (0 ms) 5: [----------] 1 test from FourCenter (0 ms total) 5: 5: [----------] 7 tests from ThreeCenter 5: [ RUN ] ThreeCenter.ListedForcesG96AngleTest 5: [ OK ] ThreeCenter.ListedForcesG96AngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesHarmonicAngleTest 5: [ OK ] ThreeCenter.ListedForcesHarmonicAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesLinearAngleTest 5: [ OK ] ThreeCenter.ListedForcesLinearAngleTest (15 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondBondTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondBondTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesCrossBondAngleTest 5: [ OK ] ThreeCenter.ListedForcesCrossBondAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesQuarticAngleTest 5: [ OK ] ThreeCenter.ListedForcesQuarticAngleTest (0 ms) 5: [ RUN ] ThreeCenter.ListedForcesRestrictedAngleTest 5: [ OK ] ThreeCenter.ListedForcesRestrictedAngleTest (0 ms) 5: [----------] 7 tests from ThreeCenter (15 ms total) 5: 5: [----------] 5 tests from TwoCenter 5: [ RUN ] TwoCenter.ListedForcesHarmonicBondTest 5: [ OK ] TwoCenter.ListedForcesHarmonicBondTest (3 ms) 5: [ RUN ] TwoCenter.ListedForcesG96BondTest 5: [ OK ] TwoCenter.ListedForcesG96BondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesCubicBondTest 5: [ OK ] TwoCenter.ListedForcesCubicBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesMorseBondTest 5: [ OK ] TwoCenter.ListedForcesMorseBondTest (0 ms) 5: [ RUN ] TwoCenter.ListedForcesFeneBondTest 5: [ OK ] TwoCenter.ListedForcesFeneBondTest (0 ms) 5: [----------] 5 tests from TwoCenter (3 ms total) 5: 5: [----------] 5 tests from ListedExampleData 5: [ RUN ] ListedExampleData.ComputeHarmonicBondForces 5: [ OK ] ListedExampleData.ComputeHarmonicBondForces (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicBondEnergies 5: [ OK ] ListedExampleData.ComputeHarmonicBondEnergies (0 ms) 5: [ RUN ] ListedExampleData.ComputeHarmonicAngleForces 5: [ OK ] ListedExampleData.ComputeHarmonicAngleForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceForces 5: [ OK ] ListedExampleData.CanReduceForces (0 ms) 5: [ RUN ] ListedExampleData.CanReduceEnergies 5: [ OK ] ListedExampleData.CanReduceEnergies (0 ms) 5: [----------] 5 tests from ListedExampleData (0 ms total) 5: 5: [----------] 1 test from LinearChainDataFixture 5: [ RUN ] LinearChainDataFixture.Multithreading 5: [ OK ] LinearChainDataFixture.Multithreading (55 ms) 5: [----------] 1 test from LinearChainDataFixture (55 ms total) 5: 5: [----------] 2 tests from ListedShims 5: [ RUN ] ListedShims.ParameterConversion 5: [ OK ] ListedShims.ParameterConversion (0 ms) 5: [ RUN ] ListedShims.GmxToNblibConversion 5: [ OK ] ListedShims.GmxToNblibConversion (0 ms) 5: [----------] 2 tests from ListedShims (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionType 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteraction 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total) 5: 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral 5: [ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth 5: [ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms) 5: [----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total) 5: 5: [----------] 1 test from ListedTransformations 5: [ RUN ] ListedTransformations.SortInteractionIndices 5: [ OK ] ListedTransformations.SortInteractionIndices (0 ms) 5: [----------] 1 test from ListedTransformations (0 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 44 tests from 22 test suites ran. (185 ms total) 5: [ PASSED ] 44 tests. 5/91 Test #5: NbLibListedForcesTests ....................... Passed 0.46 sec test 6 Start 6: NbLibSamplesTestArgon 6: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/argon-forces-integration 6: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples 6: Test timeout computed to be: 1500 6: initial forces on particle 0: x 0.000000 y 0.000000 z 0.000000 6: final forces on particle 0: x -0.412993 y -1.098256 z -0.113191 6: initial position of particle 0: x 0.794000 y 1.439000 z 0.610000 6: final position of particle 0: x 0.789162 y 1.271508 z 0.819867 6/91 Test #6: NbLibSamplesTestArgon ........................ Passed 0.13 sec test 7 Start 7: NbLibSamplesTestMethaneWater 7: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/methane-water-integration 7: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples 7: Test timeout computed to be: 1500 7: initial position of particle 0: x 0.005000 y 0.600000 z 0.244000 7: final position of particle 9: x 77.358398 y 5.324894 z -80.600098 7/91 Test #7: NbLibSamplesTestMethaneWater ................. Passed 0.29 sec test 8 Start 8: NbLibUtilTests 8: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-util-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibUtilTests.xml" 8: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/util/tests 8: Test timeout computed to be: 30 8: [==========] Running 16 tests from 2 test suites. 8: [----------] Global test environment set-up. 8: [----------] 6 tests from NBlibTest 8: [ RUN ] NBlibTest.isRealValued 8: [ OK ] NBlibTest.isRealValued (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasNan 8: [ OK ] NBlibTest.checkNumericValuesHasNan (0 ms) 8: [ RUN ] NBlibTest.checkNumericValuesHasInf 8: [ OK ] NBlibTest.checkNumericValuesHasInf (0 ms) 8: [ RUN ] NBlibTest.GeneratedVelocitiesAreCorrect 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.GeneratedVelocitiesAreCorrect (0 ms) 8: [ RUN ] NBlibTest.generateVelocitySize 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocitySize (0 ms) 8: [ RUN ] NBlibTest.generateVelocityCheckNumbers 8: Velocities were taken from a Maxwell distribution at 300 K 8: [ OK ] NBlibTest.generateVelocityCheckNumbers (0 ms) 8: [----------] 6 tests from NBlibTest (0 ms total) 8: 8: [----------] 10 tests from NblibTraitsUtils 8: [ RUN ] NblibTraitsUtils.FuseTwo 8: [ OK ] NblibTraitsUtils.FuseTwo (0 ms) 8: [ RUN ] NblibTraitsUtils.Fuse 8: [ OK ] NblibTraitsUtils.Fuse (0 ms) 8: [ RUN ] NblibTraitsUtils.Repeat 8: [ OK ] NblibTraitsUtils.Repeat (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple1 8: [ OK ] NblibTraitsUtils.FindIndexTuple1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTuple2 8: [ OK ] NblibTraitsUtils.FindIndexTuple2 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList1 8: [ OK ] NblibTraitsUtils.FindIndexTypeList1 (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeList2 8: [ OK ] NblibTraitsUtils.FindIndexTypeList2 (0 ms) 8: [ RUN ] NblibTraitsUtils.Contains 8: [ OK ] NblibTraitsUtils.Contains (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTupleRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTupleRepeated (0 ms) 8: [ RUN ] NblibTraitsUtils.FindIndexTypeListRepeated 8: [ OK ] NblibTraitsUtils.FindIndexTypeListRepeated (0 ms) 8: [----------] 10 tests from NblibTraitsUtils (0 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 16 tests from 2 test suites ran. (0 ms total) 8: [ PASSED ] 16 tests. 8/91 Test #8: NbLibUtilTests ............................... Passed 0.39 sec test 9 Start 9: NbLibSetupTests 9: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-setup-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibSetupTests.xml" 9: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 9: Test timeout computed to be: 600 9: [==========] Running 57 tests from 3 test suites. 9: [----------] Global test environment set-up. 9: [----------] 41 tests from NBlibTest 9: [ RUN ] NBlibTest.CubicBoxCannotHaveNaN 9: [ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.CubicBoxCannotHaveInf 9: [ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveNaN 9: [ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms) 9: [ RUN ] NBlibTest.RectangularBoxCannotHaveInf 9: [ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms) 9: [ RUN ] NBlibTest.CubicBoxWorks 9: [ OK ] NBlibTest.CubicBoxWorks (0 ms) 9: [ RUN ] NBlibTest.BoxEqual 9: [ OK ] NBlibTest.BoxEqual (0 ms) 9: [ RUN ] NBlibTest.NonBondedForceParamsCorrect 9: [ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms) 9: [ RUN ] NBlibTest.CanMergeInteractions 9: [ OK ] NBlibTest.CanMergeInteractions (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed 9: [ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms) 9: [ RUN ] NBlibTest.PbcHolderWorks 9: [ OK ] NBlibTest.PbcHolderWorks (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName 9: [ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms) 9: [ RUN ] NBlibTest.CanGetNumParticlesInMolecule 9: [ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNames 9: [ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms) 9: [ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed 9: [ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms) 9: [ RUN ] NBlibTest.AtWorks 9: [ OK ] NBlibTest.AtWorks (0 ms) 9: [ RUN ] NBlibTest.AtThrows 9: [ OK ] NBlibTest.AtThrows (0 ms) 9: [ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass 9: [ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms) 9: [ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName 9: [ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms) 9: [ RUN ] NBlibTest.CanAddInteractions 9: [ OK ] NBlibTest.CanAddInteractions (0 ms) 9: [ RUN ] NBlibTest.CanAddUreyBradley 9: [ OK ] NBlibTest.CanAddUreyBradley (0 ms) 9: [ RUN ] NBlibTest.TopologyHasNumParticles 9: [ OK ] NBlibTest.TopologyHasNumParticles (0 ms) 9: [ RUN ] NBlibTest.TopologyHasCharges 9: [ OK ] NBlibTest.TopologyHasCharges (0 ms) 9: [ RUN ] NBlibTest.TopologyHasMasses 9: [ OK ] NBlibTest.TopologyHasMasses (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypes 9: [ OK ] NBlibTest.TopologyHasParticleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyHasParticleTypeIds 9: [ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms) 9: [ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType 9: [ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms) 9: [ RUN ] NBlibTest.TopologyHasExclusions 9: [ OK ] NBlibTest.TopologyHasExclusions (0 ms) 9: [ RUN ] NBlibTest.TopologyHasSequencing 9: [ OK ] NBlibTest.TopologyHasSequencing (0 ms) 9: [ RUN ] NBlibTest.TopologyCanAggregateBonds 9: [ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyCanSequencePairIDs 9: [ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms) 9: [ RUN ] NBlibTest.TopologySequenceIdThrows 9: No particle O-Atom in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologySequenceIdThrows (0 ms) 9: [ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds 9: [ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractions 9: [ OK ] NBlibTest.TopologyListedInteractions (0 ms) 9: [ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes 9: [ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms) 9: [ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows 9: No particle Iron in residue SOL in molecule SOL found 9: [ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms) 9: [ RUN ] NBlibTest.toGmxExclusionBlockWorks 9: [ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms) 9: [----------] 41 tests from NBlibTest (1 ms total) 9: 9: [----------] 15 tests from NbnxmSetupTest 9: [ RUN ] NbnxmSetupTest.findNumEnergyGroups 9: [ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM 9: [ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms) 9: [ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount 9: [ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain 9: [ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms) 9: [ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv 9: [ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms) 9: [ RUN ] NbnxmSetupTest.ewaldCoeffWorks 9: [ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.updateForcerecWorks 9: [ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms) 9: [ RUN ] NbnxmSetupTest.canCheckKernelSetup 9: [ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU2XM (0 ms) 9: [ RUN ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM 9: [ OK ] NbnxmSetupTest.cannotCreateKernelSetupCPU4XM (0 ms) 9: [ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU 9: [ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms) 9: [----------] 15 tests from NbnxmSetupTest (0 ms total) 9: 9: [----------] 1 test from VirialsTest 9: [ RUN ] VirialsTest.computeVirialTensorWorks 9: [ OK ] VirialsTest.computeVirialTensorWorks (0 ms) 9: [----------] 1 test from VirialsTest (0 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 57 tests from 3 test suites ran. (1 ms total) 9: [ PASSED ] 57 tests. 9/91 Test #9: NbLibSetupTests .............................. Passed 0.35 sec test 10 Start 10: NbLibTprTests 10: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-tpr-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibTprTests.xml" 10: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 10: Test timeout computed to be: 30 10: [==========] Running 4 tests from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 4 tests from TprReaderTest 10: [ RUN ] TprReaderTest.SimDBTprIsCreated 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.SimDBTprIsCreated (62 ms) 10: [ RUN ] TprReaderTest.Spc2Reads 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Generating 1-4 interactions: fudge = 0.5 10: Number of degrees of freedom in T-Coupling group System is 9.00 10: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: NVE simulation: will use the initial temperature of 2573.591 K for 10: determining the Verlet buffer size 10: 10: 10: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads_input.mdp]: 10: You are using a plain Coulomb cut-off, which might produce artifacts. 10: You might want to consider using PME electrostatics. 10: 10: 10: 10: There were 4 NOTEs 10: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_Spc2Reads.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 10: Generated 3 of the 3 non-bonded parameter combinations 10: 10: Generated 3 of the 3 1-4 parameter combinations 10: 10: Excluding 2 bonded neighbours molecule type 'SOL' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.Spc2Reads (11 ms) 10: [ RUN ] TprReaderTest.ArgonImportedDataIsCorrect 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_ArgonImportedDataIsCorrect.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.ArgonImportedDataIsCorrect (36 ms) 10: [ RUN ] TprReaderTest.FCfromTprDataWorks 10: 10: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 10: that with the Verlet scheme, nstlist has no effect on the accuracy of 10: your simulation. 10: 10: 10: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: Setting nstcalcenergy (100) equal to nstenergy (4) 10: 10: Number of degrees of freedom in T-Coupling group System is 33.00 10: 10: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks_input.mdp]: 10: NVE simulation: will use the initial temperature of 68.810 K for 10: determining the Verlet buffer size 10: 10: 10: There were 3 NOTEs 10: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests/Testing/Temporary/TprReaderTest_FCfromTprDataWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 10: Generated 1 of the 1 non-bonded parameter combinations 10: 10: Excluding 1 bonded neighbours molecule type 'Argon' 10: 10: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 10: 10: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 10: 10: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 10: 10: Note that mdrun will redetermine rlist based on the actual pair-list setup 10: 10: This run will generate roughly 0 Mb of data 10: [ OK ] TprReaderTest.FCfromTprDataWorks (15 ms) 10: [----------] 4 tests from TprReaderTest (126 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 4 tests from 1 test suite ran. (146 ms total) 10: [ PASSED ] 4 tests. 10/91 Test #10: NbLibTprTests ................................ Passed 0.39 sec test 11 Start 11: NbLibIntegrationTests 11: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-integration-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibIntegrationTests.xml" 11: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 11: Test timeout computed to be: 600 11: [==========] Running 20 tests from 1 test suite. 11: [----------] Global test environment set-up. 11: [----------] 20 tests from NBlibTest 11: [ RUN ] NBlibTest.GmxForceCalculatorCanCompute 11: [ OK ] NBlibTest.GmxForceCalculatorCanCompute (0 ms) 11: [ RUN ] NBlibTest.ArgonVirialsAreCorrect 11: [ OK ] NBlibTest.ArgonVirialsAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonEnergiesAreCorrect 11: [ OK ] NBlibTest.ArgonEnergiesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.SpcMethanolEnergiesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolEnergiesAreCorrect (11 ms) 11: [ RUN ] NBlibTest.SpcMethanolForcesAreCorrect 11: [ OK ] NBlibTest.SpcMethanolForcesAreCorrect (3 ms) 11: [ RUN ] NBlibTest.ExpectedNumberOfForces 11: [ OK ] NBlibTest.ExpectedNumberOfForces (0 ms) 11: [ RUN ] NBlibTest.CanIntegrateSystem 11: [ OK ] NBlibTest.CanIntegrateSystem (0 ms) 11: [ RUN ] NBlibTest.UpdateChangesForces 11: [ OK ] NBlibTest.UpdateChangesForces (0 ms) 11: [ RUN ] NBlibTest.ArgonOplsaForcesAreCorrect 11: [ OK ] NBlibTest.ArgonOplsaForcesAreCorrect (0 ms) 11: [ RUN ] NBlibTest.ArgonGromos43A1ForcesAreCorrect 11: [ OK ] NBlibTest.ArgonGromos43A1ForcesAreCorrect (3 ms) 11: [ RUN ] NBlibTest.CanConstructSimulationState 11: [ OK ] NBlibTest.CanConstructSimulationState (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateNAN 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsCoordinateINF 11: [ OK ] NBlibTest.SimulationStateThrowsCoordinateINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityNAN 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityNAN (0 ms) 11: [ RUN ] NBlibTest.SimulationStateThrowsVelocityINF 11: [ OK ] NBlibTest.SimulationStateThrowsVelocityINF (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanMove 11: [ OK ] NBlibTest.SimulationStateCanMove (0 ms) 11: [ RUN ] NBlibTest.SimulationStateCanAssign 11: [ OK ] NBlibTest.SimulationStateCanAssign (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasBox 11: [ OK ] NBlibTest.SimulationStateHasBox (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectCoordinates 11: [ OK ] NBlibTest.SimulationStateHasCorrectCoordinates (0 ms) 11: [ RUN ] NBlibTest.SimulationStateHasCorrectVelocities 11: [ OK ] NBlibTest.SimulationStateHasCorrectVelocities (0 ms) 11: [----------] 20 tests from NBlibTest (22 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 20 tests from 1 test suite ran. (22 ms total) 11: [ PASSED ] 20 tests. 11/91 Test #11: NbLibIntegrationTests ........................ Passed 0.22 sec test 12 Start 12: NbLibIntegratorTests 12: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nblib-integrator-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbLibIntegratorTests.xml" 12: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/tests 12: Test timeout computed to be: 600 12: [==========] Running 1 test from 1 test suite. 12: [----------] Global test environment set-up. 12: [----------] 1 test from NBlibTest 12: [ RUN ] NBlibTest.IntegratorWorks 12: [ OK ] NBlibTest.IntegratorWorks (0 ms) 12: [----------] 1 test from NBlibTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 1 test from 1 test suite ran. (0 ms total) 12: [ PASSED ] 1 test. 12/91 Test #12: NbLibIntegratorTests ......................... Passed 0.20 sec test 13 Start 13: TestUtilsUnitTests 13: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/testutils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TestUtilsUnitTests.xml" 13: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests 13: Test timeout computed to be: 30 13: [==========] Running 59 tests from 5 test suites. 13: [----------] Global test environment set-up. 13: [----------] 10 tests from InteractiveTestHelperTest 13: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 13: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 13: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 13: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 13: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 13: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 13: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 13: [----------] 10 tests from InteractiveTestHelperTest (1 ms total) 13: 13: [----------] 34 tests from ReferenceDataTest 13: [ RUN ] ReferenceDataTest.HandlesSimpleData 13: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 13: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 13: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringBlockData 13: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesVectorData 13: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceData 13: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 13: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectData 13: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 13: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingData 13: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedData 13: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 13: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (12 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnys 13: [ OK ] ReferenceDataTest.HandlesAnys (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 13: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 13: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType 13: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 13: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 13: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 13: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 13: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 13: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 13: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 13: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 13: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesReadingValues 13: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 13: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 13: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 13: [----------] 34 tests from ReferenceDataTest (14 ms total) 13: 13: [----------] 7 tests from FloatingPointDifferenceTest 13: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 13: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 13: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 13: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 13: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 13: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 13: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 13: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 13: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 13: 13: [----------] 4 tests from FloatingPointToleranceTest 13: [ RUN ] FloatingPointToleranceTest.UlpTolerance 13: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 13: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 13: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 13: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 13: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 13: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 13: 13: [----------] 4 tests from XvgTests 13: [ RUN ] XvgTests.CreateFile 13: [ OK ] XvgTests.CreateFile (0 ms) 13: [ RUN ] XvgTests.CheckMissing 13: [ OK ] XvgTests.CheckMissing (0 ms) 13: [ RUN ] XvgTests.CheckExtra 13: [ OK ] XvgTests.CheckExtra (0 ms) 13: [ RUN ] XvgTests.ReadIncorrect 13: [ OK ] XvgTests.ReadIncorrect (0 ms) 13: [----------] 4 tests from XvgTests (0 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 59 tests from 5 test suites ran. (16 ms total) 13: [ PASSED ] 59 tests. 13/91 Test #13: TestUtilsUnitTests ........................... Passed 0.52 sec test 14 Start 14: TestUtilsMpiUnitTests 14: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 14: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/testutils/tests 14: Test timeout computed to be: 30 14: [==========] Running 1 test from 1 test suite. 14: [----------] Global test environment set-up. 14: [----------] 1 test from MpiSelfTest 14: [ RUN ] MpiSelfTest.Runs 14: [ OK ] MpiSelfTest.Runs (19 ms) 14: [----------] 1 test from MpiSelfTest (19 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 1 test from 1 test suite ran. (25 ms total) 14: [ PASSED ] 1 test. 14/91 Test #14: TestUtilsMpiUnitTests ........................ Passed 0.40 sec test 15 Start 15: UtilityUnitTests 15: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/utility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/UtilityUnitTests.xml" 15: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests 15: Test timeout computed to be: 30 15: [==========] Running 400 tests from 62 test suites. 15: [----------] Global test environment set-up. 15: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/0.Move 15: [ OK ] AllocatorTest/0.Move (0 ms) 15: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/0 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/1.Move 15: [ OK ] AllocatorTest/1.Move (0 ms) 15: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/1 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/2.Move 15: [ OK ] AllocatorTest/2.Move (0 ms) 15: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/2 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 15: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/3.Move 15: [ OK ] AllocatorTest/3.Move (0 ms) 15: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/3 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/4.Move 15: [ OK ] AllocatorTest/4.Move (0 ms) 15: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/4 (0 ms total) 15: 15: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 15: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 15: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 15: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 15: [ RUN ] AllocatorTest/5.Move 15: [ OK ] AllocatorTest/5.Move (0 ms) 15: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 15: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 15: [----------] 5 tests from AllocatorTest/5 (0 ms total) 15: 15: [----------] 1 test from AllocatorUntypedTest 15: [ RUN ] AllocatorUntypedTest.Comparison 15: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 15: [----------] 1 test from AllocatorUntypedTest (0 ms total) 15: 15: [----------] 4 tests from EmptyArrayRefTest 15: [ RUN ] EmptyArrayRefTest.IsEmpty 15: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty 15: [ OK ] EmptyArrayRefTest.ConstructFromNullptrIsEmpty (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForNullptr (0 ms) 15: [ RUN ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull 15: [ OK ] EmptyArrayRefTest.arrayRefFromArrayIsEmptyForSizeNull (0 ms) 15: [----------] 4 tests from EmptyArrayRefTest (0 ms total) 15: 15: [----------] 1 test from EmptyConstArrayRefTest 15: [ RUN ] EmptyConstArrayRefTest.IsEmpty 15: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 15: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (9 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/8 (9 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 15: 15: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 15: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 15: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 15: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 15: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 15: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 15: 15: [----------] 8 tests from BoolType 15: [ RUN ] BoolType.ImplicitConversion 15: [ OK ] BoolType.ImplicitConversion (0 ms) 15: [ RUN ] BoolType.FalseByDefault 15: [ OK ] BoolType.FalseByDefault (0 ms) 15: [ RUN ] BoolType.Assignment 15: [ OK ] BoolType.Assignment (0 ms) 15: [ RUN ] BoolType.Copy 15: [ OK ] BoolType.Copy (0 ms) 15: [ RUN ] BoolType.ArrayRefCanBeCreated 15: [ OK ] BoolType.ArrayRefCanBeCreated (0 ms) 15: [ RUN ] BoolType.CanBeCastToBool 15: [ OK ] BoolType.CanBeCastToBool (0 ms) 15: [ RUN ] BoolType.HasSizeOfBool 15: [ OK ] BoolType.HasSizeOfBool (0 ms) 15: [ RUN ] BoolType.HasAlignmentOfBool 15: [ OK ] BoolType.HasAlignmentOfBool (0 ms) 15: [----------] 8 tests from BoolType (0 ms total) 15: 15: [----------] 4 tests from ArrayRefFromBoolTypeVector 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.Works 15: [ OK ] ArrayRefFromBoolTypeVector.Works (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty 15: [ OK ] ArrayRefFromBoolTypeVector.CanConstructConstEmpty (0 ms) 15: [ RUN ] ArrayRefFromBoolTypeVector.ConstWorks 15: [ OK ] ArrayRefFromBoolTypeVector.ConstWorks (0 ms) 15: [----------] 4 tests from ArrayRefFromBoolTypeVector (0 ms total) 15: 15: [----------] 7 tests from CStringUtilityTest 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms) 15: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength 15: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms) 15: [ RUN ] CStringUtilityTest.strip_comment 15: [ OK ] CStringUtilityTest.strip_comment (0 ms) 15: [ RUN ] CStringUtilityTest.upstring 15: [ OK ] CStringUtilityTest.upstring (0 ms) 15: [ RUN ] CStringUtilityTest.ltrim 15: [ OK ] CStringUtilityTest.ltrim (0 ms) 15: [ RUN ] CStringUtilityTest.rtrim 15: [ OK ] CStringUtilityTest.rtrim (0 ms) 15: [ RUN ] CStringUtilityTest.trim 15: [ OK ] CStringUtilityTest.trim (0 ms) 15: [----------] 7 tests from CStringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from DefaultInitializationAllocator 15: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms) 15: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization 15: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms) 15: [----------] 2 tests from DefaultInitializationAllocator (0 ms total) 15: 15: [----------] 4 tests from EnumerationHelpersTest 15: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks 15: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms) 15: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe 15: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms) 15: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks 15: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms) 15: [----------] 4 tests from EnumerationHelpersTest (0 ms total) 15: 15: [----------] 9 tests from FixedCapacityVectorTest 15: [ RUN ] FixedCapacityVectorTest.IsEmpty 15: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PushWorks 15: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.PopWorks 15: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ClearWorks 15: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks 15: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.AtThrows 15: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms) 15: [ RUN ] FixedCapacityVectorTest.IteratorWorks 15: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks 15: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms) 15: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks 15: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms) 15: [----------] 9 tests from FixedCapacityVectorTest (0 ms total) 15: 15: [----------] 5 tests from InMemorySerializerTest 15: [ RUN ] InMemorySerializerTest.Roundtrip 15: [ OK ] InMemorySerializerTest.Roundtrip (0 ms) 15: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap 15: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap 15: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms) 15: [ RUN ] InMemorySerializerTest.SizeIsCorrect 15: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms) 15: [----------] 5 tests from InMemorySerializerTest (0 ms total) 15: 15: [----------] 4 tests from KeyValueTreeSerializerTest 15: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 15: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 15: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 15: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 15: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 15: [----------] 4 tests from KeyValueTreeSerializerTest (0 ms total) 15: 15: [----------] 7 tests from TreeValueTransformTest 15: [ RUN ] TreeValueTransformTest.SimpleTransforms 15: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 15: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 15: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 15: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (13 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromString 15: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 15: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 15: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 15: [ RUN ] TreeValueTransformTest.ScopedTransformRules 15: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 15: [ RUN ] TreeValueTransformTest.CanAssignUserMultiValue 15: [ OK ] TreeValueTransformTest.CanAssignUserMultiValue (0 ms) 15: [----------] 7 tests from TreeValueTransformTest (13 ms total) 15: 15: [----------] 1 test from TreeValueTransformErrorTest 15: [ RUN ] TreeValueTransformErrorTest.ConversionError 15: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 15: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 15: 15: [----------] 9 tests from ListOfLists 15: [ RUN ] ListOfLists.EmptyListOfListsWorks 15: [ OK ] ListOfLists.EmptyListOfListsWorks (0 ms) 15: [ RUN ] ListOfLists.AppendWorks 15: [ OK ] ListOfLists.AppendWorks (0 ms) 15: [ RUN ] ListOfLists.EmptyListWorks 15: [ OK ] ListOfLists.EmptyListWorks (0 ms) 15: [ RUN ] ListOfLists.AppendAccessWorks 15: [ OK ] ListOfLists.AppendAccessWorks (0 ms) 15: [ RUN ] ListOfLists.ClearWorks 15: [ OK ] ListOfLists.ClearWorks (0 ms) 15: [ RUN ] ListOfLists.OutOfRangeAccessThrows 15: [ OK ] ListOfLists.OutOfRangeAccessThrows (0 ms) 15: [ RUN ] ListOfLists.FrontAndBackWork 15: [ OK ] ListOfLists.FrontAndBackWork (0 ms) 15: [ RUN ] ListOfLists.ExtractsAndRestores 15: [ OK ] ListOfLists.ExtractsAndRestores (0 ms) 15: [ RUN ] ListOfLists.AppendsListOfListsWithOffset 15: [ OK ] ListOfLists.AppendsListOfListsWithOffset (0 ms) 15: [----------] 9 tests from ListOfLists (0 ms total) 15: 15: [----------] 7 tests from LoggerTest 15: [ RUN ] LoggerTest.EmptyLoggerWorks 15: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToStream 15: [ OK ] LoggerTest.LogsToStream (0 ms) 15: [ RUN ] LoggerTest.LogsToFile 15: [ OK ] LoggerTest.LogsToFile (0 ms) 15: [ RUN ] LoggerTest.LevelFilteringWorks 15: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 15: [ RUN ] LoggerTest.LogsToMultipleStreams 15: [ OK ] LoggerTest.LogsToMultipleStreams (6 ms) 15: [ RUN ] LoggerTest.LogsToMultipleFiles 15: [ OK ] LoggerTest.LogsToMultipleFiles (0 ms) 15: [ RUN ] LoggerTest.LogsToStreamAndFile 15: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms) 15: [----------] 7 tests from LoggerTest (7 ms total) 15: 15: [----------] 7 tests from MessageStringCollectorTest 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesNoContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext 15: [ OK ] MessageStringCollectorTest.CanAddAndClearMessagesWithContext (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessages 15: [ OK ] MessageStringCollectorTest.CanAddStringMessages (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddCharMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddCharMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanAddStringMessagesConditionally 15: [ OK ] MessageStringCollectorTest.CanAddStringMessagesConditionally (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveConstruct 15: [ OK ] MessageStringCollectorTest.CanMoveConstruct (0 ms) 15: [ RUN ] MessageStringCollectorTest.CanMoveAssign 15: [ OK ] MessageStringCollectorTest.CanMoveAssign (0 ms) 15: [----------] 7 tests from MessageStringCollectorTest (0 ms total) 15: 15: [----------] 1 test from PathTest 15: [ RUN ] PathTest.StripSourcePrefixWorks 15: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 15: [----------] 1 test from PathTest (0 ms total) 15: 15: [----------] 2 tests from PhysicalNodeCommunicatorTest 15: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 15: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 15: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 15: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 15: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 15: 15: [----------] 5 tests from Range 15: [ RUN ] Range.EmptyRangeWorks 15: [ OK ] Range.EmptyRangeWorks (0 ms) 15: [ RUN ] Range.NonEmptyRangeWorks 15: [ OK ] Range.NonEmptyRangeWorks (0 ms) 15: [ RUN ] Range.BeginEnd 15: [ OK ] Range.BeginEnd (0 ms) 15: [ RUN ] Range.IsInRangeWorks 15: [ OK ] Range.IsInRangeWorks (0 ms) 15: [ RUN ] Range.IteratorWorks 15: [ OK ] Range.IteratorWorks (0 ms) 15: [----------] 5 tests from Range (0 ms total) 15: 15: [----------] 7 tests from StringConvert 15: [ RUN ] StringConvert.NoResultFromEptyString 15: [ OK ] StringConvert.NoResultFromEptyString (0 ms) 15: [ RUN ] StringConvert.ThreeFloatsSuccessfully 15: [ OK ] StringConvert.ThreeFloatsSuccessfully (0 ms) 15: [ RUN ] StringConvert.OneIntSucessfully 15: [ OK ] StringConvert.OneIntSucessfully (0 ms) 15: [ RUN ] StringConvert.FloatAsStringToIntArrayThrows 15: [ OK ] StringConvert.FloatAsStringToIntArrayThrows (0 ms) 15: [ RUN ] StringConvert.ThrowsWhenWrongSize 15: [ OK ] StringConvert.ThrowsWhenWrongSize (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayThrows 15: [ OK ] StringConvert.StringIdentityTransformWithArrayThrows (0 ms) 15: [ RUN ] StringConvert.StringIdentityTransformWithArrayOkay 15: [ OK ] StringConvert.StringIdentityTransformWithArrayOkay (0 ms) 15: [----------] 7 tests from StringConvert (0 ms total) 15: 15: [----------] 7 tests from StringToEnumValueConverterTest 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithoutStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.ExactStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping 15: [ OK ] StringToEnumValueConverterTest.CaseAndDashInsensitiveStringComparisonWorksWithStripping (0 ms) 15: [ RUN ] StringToEnumValueConverterTest.CustomConverterWorks 15: [ OK ] StringToEnumValueConverterTest.CustomConverterWorks (0 ms) 15: [----------] 7 tests from StringToEnumValueConverterTest (0 ms total) 15: 15: [----------] 9 tests from StringUtilityTest 15: [ RUN ] StringUtilityTest.StartsWith 15: [ OK ] StringUtilityTest.StartsWith (0 ms) 15: [ RUN ] StringUtilityTest.EndsWith 15: [ OK ] StringUtilityTest.EndsWith (0 ms) 15: [ RUN ] StringUtilityTest.StripSuffixIfPresent 15: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 15: [ RUN ] StringUtilityTest.StripString 15: [ OK ] StringUtilityTest.StripString (0 ms) 15: [ RUN ] StringUtilityTest.SplitString 15: [ OK ] StringUtilityTest.SplitString (0 ms) 15: [ RUN ] StringUtilityTest.SplitDelimitedString 15: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 15: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms) 15: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength 15: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms) 15: [----------] 9 tests from StringUtilityTest (0 ms total) 15: 15: [----------] 2 tests from FormatStringTest 15: [ RUN ] FormatStringTest.HandlesBasicFormatting 15: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 15: [ RUN ] FormatStringTest.HandlesLongStrings 15: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 15: [----------] 2 tests from FormatStringTest (0 ms total) 15: 15: [----------] 1 test from StringFormatterTest 15: [ RUN ] StringFormatterTest.HandlesBasicFormatting 15: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 15: [----------] 1 test from StringFormatterTest (0 ms total) 15: 15: [----------] 1 test from formatAndJoinTest 15: [ RUN ] formatAndJoinTest.Works 15: [ OK ] formatAndJoinTest.Works (0 ms) 15: [----------] 1 test from formatAndJoinTest (0 ms total) 15: 15: [----------] 1 test from JoinStringsTest 15: [ RUN ] JoinStringsTest.Works 15: [ OK ] JoinStringsTest.Works (0 ms) 15: [----------] 1 test from JoinStringsTest (0 ms total) 15: 15: [----------] 6 tests from ReplaceAllTest 15: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 15: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesNoMatches 15: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 15: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 15: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 15: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 15: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 15: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 15: [----------] 6 tests from ReplaceAllTest (0 ms total) 15: 15: [----------] 10 tests from TextLineWrapperTest 15: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 15: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 15: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 15: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectly 15: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndent 15: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 15: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 15: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 15: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 15: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (6 ms) 15: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 15: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 15: [----------] 10 tests from TextLineWrapperTest (7 ms total) 15: 15: [----------] 3 tests from TemplateMPTest 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnum 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnum (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionBool (0 ms) 15: [ RUN ] TemplateMPTest.DispatchTemplatedFunctionEnumBool 15: [ OK ] TemplateMPTest.DispatchTemplatedFunctionEnumBool (0 ms) 15: [----------] 3 tests from TemplateMPTest (0 ms total) 15: 15: [----------] 6 tests from TextWriterTest 15: [ RUN ] TextWriterTest.WritesLines 15: [ OK ] TextWriterTest.WritesLines (0 ms) 15: [ RUN ] TextWriterTest.WritesLinesInParts 15: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 15: [ RUN ] TextWriterTest.WritesWrappedLines 15: [ OK ] TextWriterTest.WritesWrappedLines (7 ms) 15: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 15: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 15: [ RUN ] TextWriterTest.TracksNewlines 15: [ OK ] TextWriterTest.TracksNewlines (0 ms) 15: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 15: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 15: [----------] 6 tests from TextWriterTest (8 ms total) 15: 15: [----------] 1 test from TypeTraitsTest 15: [ RUN ] TypeTraitsTest.IsIntegralConstant 15: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 15: [----------] 1 test from TypeTraitsTest (0 ms total) 15: 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 15: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 15: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 15: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 15: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 15: 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 15: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 15: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 15: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 15: 15: [----------] 11 tests from WithInputPaths/PathSearchTest 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/0 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/1 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/2 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/3 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/4 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/5 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/6 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/7 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/8 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/9 (0 ms) 15: [ RUN ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 15: [ OK ] WithInputPaths/PathSearchTest.SearchOperationsWork/10 (0 ms) 15: [----------] 11 tests from WithInputPaths/PathSearchTest (0 ms total) 15: 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 15: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 15: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 15: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 400 tests from 62 test suites ran. (50 ms total) 15: [ PASSED ] 400 tests. 15: 15: YOU HAVE 1 DISABLED TEST 15: 15/91 Test #15: UtilityUnitTests ............................. Passed 0.20 sec test 16 Start 16: UtilityMpiUnitTests 16: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/utility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/UtilityMpiUnitTests.xml" 16: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/utility/tests 16: Test timeout computed to be: 30 16: [==========] Running 2 tests from 1 test suite. 16: [----------] Global test environment set-up. 16: [----------] 2 tests from PhysicalNodeCommunicatorTest 16: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 16: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (72 ms) 16: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 16: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 16: [----------] 2 tests from PhysicalNodeCommunicatorTest (104 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 2 tests from 1 test suite ran. (116 ms total) 16: [ PASSED ] 2 tests. 16/91 Test #16: UtilityMpiUnitTests .......................... Passed 0.74 sec test 17 Start 17: GmxlibTests 17: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nonbonded-fep-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxlibTests.xml" 17: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxlib/nonbonded/tests 17: Test timeout computed to be: 30 17: [==========] Running 78 tests from 2 test suites. 17: [----------] Global test environment set-up. 17: [----------] 72 tests from NBInteraction/NonbondedFepTest 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/0 (7 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/1 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/5 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/6 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/6 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/7 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/7 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/8 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/8 (4 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/9 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/9 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/10 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/10 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/11 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/11 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/12 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/12 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/13 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/13 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/14 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/14 (1 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/15 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/15 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/16 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/16 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/17 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/17 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/18 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/18 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/19 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/19 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/20 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/20 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/21 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/21 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/22 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/22 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/23 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/23 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/24 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/24 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/25 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/25 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/26 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/26 (11 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/27 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/27 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/28 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/28 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/29 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/29 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/30 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/30 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/31 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/31 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/32 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/32 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/33 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/33 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/34 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/34 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/35 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/35 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/36 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/36 (6 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/37 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/37 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/38 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/38 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/39 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/39 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/40 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/40 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/41 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/41 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/42 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/42 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/43 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/43 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/44 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/44 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/45 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/45 (4 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/46 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/46 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/47 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/47 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/48 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/48 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/49 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/49 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/50 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/50 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/51 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/51 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/52 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/52 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/53 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/53 (15 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/54 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/54 (3 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/55 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/55 (8 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/56 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/56 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/57 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/57 (7 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/58 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/58 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/59 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/59 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/60 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/60 (15 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/61 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/61 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/62 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/62 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/63 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/63 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/64 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/64 (3 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/65 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/65 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/66 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/66 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/67 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/67 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/68 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/68 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/69 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/69 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/70 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/70 (0 ms) 17: [ RUN ] NBInteraction/NonbondedFepTest.testKernel/71 17: [ OK ] NBInteraction/NonbondedFepTest.testKernel/71 (0 ms) 17: [----------] 72 tests from NBInteraction/NonbondedFepTest (95 ms total) 17: 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/0 (15 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/1 (3 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/2 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/3 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/4 (0 ms) 17: [ RUN ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 17: [ OK ] NBInteractionShortDistance/NonbondedFepTest.testKernel/5 (0 ms) 17: [----------] 6 tests from NBInteractionShortDistance/NonbondedFepTest (19 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 78 tests from 2 test suites ran. (115 ms total) 17: [ PASSED ] 78 tests. 17/91 Test #17: GmxlibTests .................................. Passed 0.32 sec test 18 Start 18: MdlibUnitTest 18: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdlib-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdlibUnitTest.xml" 18: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests 18: Test timeout computed to be: 30 18: [==========] Running 999 tests from 25 test suites. 18: [----------] Global test environment set-up. 18: [----------] 2 tests from EffectiveAtomDensity 18: [ RUN ] EffectiveAtomDensity.VolumeIndependence 18: [ OK ] EffectiveAtomDensity.VolumeIndependence (24 ms) 18: [ RUN ] EffectiveAtomDensity.WeightingWorks 18: [ OK ] EffectiveAtomDensity.WeightingWorks (0 ms) 18: [----------] 2 tests from EffectiveAtomDensity (24 ms total) 18: 18: [----------] 2 tests from AtomNonbondedAndKineticProperties 18: [ RUN ] AtomNonbondedAndKineticProperties.IsAccurate 18: [ OK ] AtomNonbondedAndKineticProperties.IsAccurate (0 ms) 18: [ RUN ] AtomNonbondedAndKineticProperties.ConstraintsWork 18: [ OK ] AtomNonbondedAndKineticProperties.ConstraintsWork (0 ms) 18: [----------] 2 tests from AtomNonbondedAndKineticProperties (0 ms total) 18: 18: [----------] 1 test from VerletBufferConstraintTest 18: [ RUN ] VerletBufferConstraintTest.EqualMasses 18: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 18: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 18: 18: [----------] 6 tests from CalcvirTest 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBox 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBox (3 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew 18: [ OK ] CalcvirTest.CanCalculateVirialAllAtomsInBoxScrew (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewX (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewY (0 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewZ (15 ms) 18: [ RUN ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ 18: [ OK ] CalcvirTest.CanCalculateVirialAtomsOutOfBoxScrewXYZ (0 ms) 18: [----------] 6 tests from CalcvirTest (20 ms total) 18: 18: [----------] 2 tests from PrEbinTest 18: [ RUN ] PrEbinTest.HandlesAverages 18: [ OK ] PrEbinTest.HandlesAverages (0 ms) 18: [ RUN ] PrEbinTest.HandlesEmptyAverages 18: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms) 18: [----------] 2 tests from PrEbinTest (0 ms total) 18: 18: [----------] 3 tests from EnergyDriftTracker 18: [ RUN ] EnergyDriftTracker.emptyWorks 18: [ OK ] EnergyDriftTracker.emptyWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.onePointWorks 18: [ OK ] EnergyDriftTracker.onePointWorks (0 ms) 18: [ RUN ] EnergyDriftTracker.manyPointsWorks 18: [ OK ] EnergyDriftTracker.manyPointsWorks (0 ms) 18: [----------] 3 tests from EnergyDriftTracker (0 ms total) 18: 18: [----------] 4 tests from ShakeTest 18: [ RUN ] ShakeTest.ConstrainsOneBond 18: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 18: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 18: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 18: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 18: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 18: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 18: [----------] 4 tests from ShakeTest (0 ms total) 18: 18: [----------] 1 test from NullSignalTest 18: [ RUN ] NullSignalTest.NullSignallerWorks 18: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 18: [----------] 1 test from NullSignalTest (0 ms total) 18: 18: [----------] 7 tests from SignalTest 18: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 18: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 18: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 18: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 18: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 18: [----------] 7 tests from SignalTest (0 ms total) 18: 18: [----------] 13 tests from UpdateGroupsTest 18: [ RUN ] UpdateGroupsTest.WithEthaneUA 18: [ OK ] UpdateGroupsTest.WithEthaneUA (0 ms) 18: [ RUN ] UpdateGroupsTest.WithMethane 18: [ OK ] UpdateGroupsTest.WithMethane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithEthane 18: [ OK ] UpdateGroupsTest.WithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithEthane (0 ms) 18: [ RUN ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups 18: [ OK ] UpdateGroupsTest.WithButaneUALogsThatUnsuitableForUpdateGroups (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterThreeSite 18: [ OK ] UpdateGroupsTest.WithWaterThreeSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFourSite 18: [ OK ] UpdateGroupsTest.WithWaterFourSite (0 ms) 18: [ RUN ] UpdateGroupsTest.WithFourAtomsWithSettle 18: [ OK ] UpdateGroupsTest.WithFourAtomsWithSettle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.WithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle 18: [ OK ] UpdateGroupsTest.CheckRadiusCalculationAtDifferentTemperaturesWithWaterFlexAngle (0 ms) 18: [ RUN ] UpdateGroupsTest.WithTwoMoltypes 18: [ OK ] UpdateGroupsTest.WithTwoMoltypes (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenSizesAreInvalid 18: [ OK ] UpdateGroupsTest.LogsWhenSizesAreInvalid (0 ms) 18: [ RUN ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful 18: [ OK ] UpdateGroupsTest.LogsWhenUpdateGroupsAreNotUseful (0 ms) 18: [----------] 13 tests from UpdateGroupsTest (0 ms total) 18: 18: [----------] 1 test from UpdateGroupsCog 18: [ RUN ] UpdateGroupsCog.ComputesCogs 18: [ OK ] UpdateGroupsCog.ComputesCogs (0 ms) 18: [----------] 1 test from UpdateGroupsCog (0 ms total) 18: 18: [----------] 2 tests from WholeMoleculeTransform 18: [ RUN ] WholeMoleculeTransform.MakesMoleculesWhole 18: [ OK ] WholeMoleculeTransform.MakesMoleculesWhole (0 ms) 18: [ RUN ] WholeMoleculeTransform.HandlesReordering 18: [ OK ] WholeMoleculeTransform.HandlesReordering (0 ms) 18: [----------] 2 tests from WholeMoleculeTransform (0 ms total) 18: 18: [----------] 14 tests from WithParameters/ConstraintsTest 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/1 (26 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/9 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/12 (132 ms) 18: [ RUN ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 18: [ OK ] WithParameters/ConstraintsTest.SatisfiesConstraints/13 (50 ms) 18: [----------] 14 tests from WithParameters/ConstraintsTest (212 ms total) 18: 18: [----------] 11 tests from WithParameters/EnergyOutputTest 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (15 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (22 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3 18: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (0 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file 18: Reading energy frame 0 time 10.100 Reading energy frame 1 time 27.500 Reading energy frame 2 time 44.900 Reading energy frame 3 time 62.300 Reading energy frame 4 time 79.700 Reading energy frame 5 time 97.100 Reading energy frame 6 time 114.500 Reading energy frame 7 time 131.900 Reading energy frame 8 time 149.300 Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (74 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (1 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (17 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (5 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (11 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (23 ms) 18: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10 18: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file 18: Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (0 ms) 18: [----------] 11 tests from WithParameters/EnergyOutputTest (188 ms total) 18: 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms) 18: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 18: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms) 18: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (0 ms total) 18: 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms) 18: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 18: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms) 18: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (0 ms total) 18: 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/0 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/1 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/2 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/3 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/4 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/5 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/6 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/7 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/8 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/9 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/10 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/11 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/12 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/13 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/14 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/15 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/16 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/17 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/18 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/19 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/20 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/21 (0 ms) 18: [ RUN ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 18: [ OK ] WithParameters/FreeEnergyParameterTest.CorrectLambdas/22 (0 ms) 18: [----------] 23 tests from WithParameters/FreeEnergyParameterTest (0 ms total) 18: 18: [----------] 16 tests from WithParameters/LeapFrogTest 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (21 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (45 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (12 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (4 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (11 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (0 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (26 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (16 ms) 18: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15 18: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (0 ms) 18: [----------] 16 tests from WithParameters/LeapFrogTest (143 ms total) 18: 18: [----------] 140 tests from Cubic/ParrRahmTest 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (17 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (19 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (23 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (19 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (15 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (19 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (19 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_1 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_general_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_0 (23 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__100 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_cubic_box_10000_boxv_100 (2 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_0 (12 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1e_07 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_1 (23 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_cubic_box_10000_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_2_5_boxv_100 (3 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_general_shape_cubic_box_10000_boxv_100 (23 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__100 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_0 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_1 (0 ms) 18: [ RUN ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 18: [ OK ] Cubic/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_cubic_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Cubic/ParrRahmTest (261 ms total) 18: 18: [----------] 140 tests from Rectilinear/ParrRahmTest 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (19 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (4 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (2 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (5 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_2_5_boxv_100 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_general_shape_rect_box_10000_boxv_100 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1e_07 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv__1e_07 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_2_5_boxv_100 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rect_box_10000_boxv_100 (6 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_1 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv__1e_07 (3 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rect_box_10000_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__100 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_0 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_1 (0 ms) 18: [ RUN ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 18: [ OK ] Rectilinear/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rect_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Rectilinear/ParrRahmTest (144 ms total) 18: 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (7 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (7 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (7 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (4 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (12 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (17 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (18 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__100 (19 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (15 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (23 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1 (23 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv__1e_07 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1e_07 (19 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_1 (19 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_0 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__100 (23 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1 (3 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1e_07 (15 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__100 (17 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_0 (10 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_1 (11 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rds_box_10000_boxv_100 (19 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1 (5 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv__1e_07 (6 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_1 (7 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__100 (1 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1e_07 (1 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rds_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 18: [ OK ] RhombDodecXYSquare/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rds_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYSquare/ParrRahmTest (407 ms total) 18: 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (11 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__100 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_rdh_box_10000_boxv_100 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv__1e_07 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_2_5_boxv_100 (7 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_0 (1 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1e_07 (2 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_2_5_boxv_100 (3 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__100 (1 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_general_shape_rdh_box_10000_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_2_5_boxv_100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__100 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_0 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_1 (0 ms) 18: [ RUN ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 18: [ OK ] RhombDodecXYHex/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_rdh_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from RhombDodecXYHex/ParrRahmTest (75 ms total) 18: 18: [----------] 140 tests from TruncOct/ParrRahmTest 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (7 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (7 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (3 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (3 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__100 (6 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1 (3 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv__1e_07 (11 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_1 (3 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__100 (15 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1e_07 (3 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_1 (11 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_to_box_10000_boxv_100 (3 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__100 (15 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_general_shape_to_box_10000_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_2_5_boxv_100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__100 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_0 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_1 (0 ms) 18: [ RUN ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 18: [ OK ] TruncOct/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_to_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from TruncOct/ParrRahmTest (104 ms total) 18: 18: [----------] 140 tests from Other/ParrRahmTest 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Isotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1e_07 (4 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_part_unif_diag_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_diagonal_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_general_shape_other_box_10000_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_2_5_boxv_100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__100 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv__1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_0 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1e_07 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_1 (0 ms) 18: [ RUN ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 18: [ OK ] Other/ParrRahmTest.Works/Anisotropic_pmt_extreme_shape_other_box_10000_boxv_100 (0 ms) 18: [----------] 140 tests from Other/ParrRahmTest (8 ms total) 18: 18: [----------] 13 tests from WithParameters/SettleTest 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (24 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 18: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 18: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 18: [----------] 13 tests from WithParameters/SettleTest (28 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 999 tests from 25 test suites ran. (1622 ms total) 18: [ PASSED ] 999 tests. 18/91 Test #18: MdlibUnitTest ................................ Passed 2.24 sec test 19 Start 19: AwhTest 19: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/awh-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/AwhTest.xml" 19: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/awh/tests 19: Test timeout computed to be: 30 19: [==========] Running 25 tests from 9 test suites. 19: [----------] Global test environment set-up. 19: [----------] 3 tests from SerializationTest 19: [ RUN ] SerializationTest.CanSerializeDimParams 19: [ OK ] SerializationTest.CanSerializeDimParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeBiasParams 19: [ OK ] SerializationTest.CanSerializeBiasParams (0 ms) 19: [ RUN ] SerializationTest.CanSerializeAwhParams 19: [ OK ] SerializationTest.CanSerializeAwhParams (0 ms) 19: [----------] 3 tests from SerializationTest (0 ms total) 19: 19: [----------] 1 test from BiasTest 19: [ RUN ] BiasTest.DetectsCovering 19: [ OK ] BiasTest.DetectsCovering (0 ms) 19: [----------] 1 test from BiasTest (0 ms total) 19: 19: [----------] 1 test from biasGridTest 19: [ RUN ] biasGridTest.neighborhood 19: [ OK ] biasGridTest.neighborhood (0 ms) 19: [----------] 1 test from biasGridTest (0 ms total) 19: 19: [----------] 2 tests from BiasFepLambdaStateTest 19: [ RUN ] BiasFepLambdaStateTest.DetectsCovering 19: [ OK ] BiasFepLambdaStateTest.DetectsCovering (1 ms) 19: [ RUN ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy 19: [ OK ] BiasFepLambdaStateTest.DetectsLargeNegativeForeignEnergy (0 ms) 19: [----------] 2 tests from BiasFepLambdaStateTest (2 ms total) 19: 19: [----------] 8 tests from WithParameters/BiasTest 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/0 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/1 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/2 (12 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/3 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/4 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/5 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/6 (0 ms) 19: [ RUN ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 19: [ OK ] WithParameters/BiasTest.ForcesBiasPmfWeightSum/7 (0 ms) 19: [----------] 8 tests from WithParameters/BiasTest (15 ms total) 19: 19: [----------] 2 tests from WithParameters/BiasStateTest 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 19: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 19: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 19: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 19: 19: [----------] 1 test from WithParameters/UserInputTest 19: [ RUN ] WithParameters/UserInputTest.ParsesUser3DInput/0 19: [ OK ] WithParameters/UserInputTest.ParsesUser3DInput/0 (0 ms) 19: [----------] 1 test from WithParameters/UserInputTest (0 ms total) 19: 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/0 (11 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/1 (11 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/2 (15 ms) 19: [ RUN ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 19: [ OK ] WithParameters/BiasFepLambdaStateTest.ForcesBiasPmf/3 (7 ms) 19: [----------] 4 tests from WithParameters/BiasFepLambdaStateTest (48 ms total) 19: 19: [----------] 3 tests from WithParameters/FrictionMetricTest 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/0 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/0 (0 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/1 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/1 (8 ms) 19: [ RUN ] WithParameters/FrictionMetricTest.FrictionMetric/2 19: [ OK ] WithParameters/FrictionMetricTest.FrictionMetric/2 (47 ms) 19: [----------] 3 tests from WithParameters/FrictionMetricTest (58 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 25 tests from 9 test suites ran. (125 ms total) 19: [ PASSED ] 25 tests. 19/91 Test #19: AwhTest ...................................... Passed 0.33 sec test 20 Start 20: DensityFittingAppliedForcesUnitTest 20: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/density_fitting_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/DensityFittingAppliedForcesUnitTest.xml" 20: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/densityfitting/tests 20: Test timeout computed to be: 30 20: [==========] Running 18 tests from 4 test suites. 20: [----------] Global test environment set-up. 20: [----------] 2 tests from DensityFittingTest 20: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows 20: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (0 ms) 20: [ RUN ] DensityFittingTest.SingleAtom 20: [ OK ] DensityFittingTest.SingleAtom (0 ms) 20: [----------] 2 tests from DensityFittingTest (0 ms total) 20: 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest 20: [ RUN ] DensityFittingAmplitudeLookupTest.Unity 20: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Charge 20: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.Masses 20: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms) 20: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct 20: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms) 20: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total) 20: 20: [----------] 1 test from DensityFittingForceProviderState 20: [ RUN ] DensityFittingForceProviderState.RoundTripSaving 20: [ OK ] DensityFittingForceProviderState.RoundTripSaving (0 ms) 20: [----------] 1 test from DensityFittingForceProviderState (0 ms total) 20: 20: [----------] 8 tests from DensityFittingOptionsTest 20: [ RUN ] DensityFittingOptionsTest.DefaultParameters 20: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OptionSetsActive 20: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive 20: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive 20: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms) 20: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup 20: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 20: [ RUN ] DensityFittingOptionsTest.InternalsToKvt 20: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms) 20: [ RUN ] DensityFittingOptionsTest.KvtToInternal 20: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms) 20: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent 20: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms) 20: [----------] 8 tests from DensityFittingOptionsTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 18 tests from 4 test suites ran. (1 ms total) 20: [ PASSED ] 18 tests. 20/91 Test #20: DensityFittingAppliedForcesUnitTest .......... Passed 0.29 sec test 21 Start 21: QMMMAppliedForcesUnitTest 21: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/qmmm_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/QMMMAppliedForcesUnitTest.xml" 21: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests 21: Test timeout computed to be: 30 21: [==========] Running 21 tests from 5 test suites. 21: [----------] Global test environment set-up. 21: [----------] 3 tests from QMMMInputGeneratorTest 21: [ RUN ] QMMMInputGeneratorTest.CanConstruct 21: [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) 21: [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink 21: [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) 21: [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) 21: 21: [----------] 7 tests from QMMMTopologyPreprocessorTest 21: [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct 21: [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -287965217 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (27 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -67488271 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 21.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -1083777049 21: 21: Generated 10 of the 10 non-bonded parameter combinations 21: 21: Generated 10 of the 10 1-4 parameter combinations 21: 21: Excluding 2 bonded neighbours molecule type 'SOL' 21: Analysing residue names: 21: There are: 4 Water residues 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (22 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: Number of degrees of freedom in T-Coupling group rest is 63.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 129.093 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to -33446 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (47 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Generating 1-4 interactions: fudge = 0.5 21: 21: NOTE 2 [file unknown]: 21: You are using constraints on all bonds, whereas the forcefield has been 21: parametrized only with constraints involving hydrogen atoms. We suggest 21: using constraints = h-bonds instead, this will also improve performance. 21: 21: 21: NOTE 3 [file unknown]: 21: For energy conservation with LINCS, lincs_iter should be 2 or larger. 21: 21: 21: Number of degrees of freedom in T-Coupling group rest is 42.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: NVE simulation: will use the initial temperature of 193.640 K for 21: determining the Verlet buffer size 21: 21: 21: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 5 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to 2104986399 21: 21: Generated 2145 of the 2145 non-bonded parameter combinations 21: 21: Generated 2145 of the 2145 1-4 parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 21: 21: turning all bonds into constraints... 21: Analysing residue names: 21: There are: 3 Protein residues 21: Analysing Protein... 21: 21: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K 21: 21: Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm 21: 21: Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm 21: 21: Note that mdrun will redetermine rlist based on the actual pair-list setup 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (52 ms) 21: [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites 21: 21: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: For a correct single-point energy evaluation with nsteps = 0, use 21: continuation = yes to avoid constraining the input coordinates. 21: 21: Number of degrees of freedom in T-Coupling group rest is 45.00 21: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 21: 21: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: NVE simulation with an initial temperature of zero: will use a Verlet 21: buffer of 10%. Check your energy drift! 21: 21: 21: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: 21: You are using a plain Coulomb cut-off, which might produce artifacts. 21: You might want to consider using PME electrostatics. 21: 21: 21: 21: There were 3 NOTEs 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 21: Setting the LD random seed to 2108929007 21: 21: Generated 3 of the 6 non-bonded parameter combinations 21: 21: Excluding 3 bonded neighbours molecule type 'VSTEST' 21: 21: Cleaning up constraints and constant bonded interactions with virtual sites 21: Analysing residue names: 21: There are: 1 Other residues 21: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 21: 21: This run will generate roughly 0 Mb of data 21: [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (23 ms) 21: [----------] 7 tests from QMMMTopologyPreprocessorTest (176 ms total) 21: 21: [----------] 9 tests from QMMMOptionsTest 21: [ RUN ] QMMMOptionsTest.DefaultParameters 21: [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) 21: [ RUN ] QMMMOptionsTest.OptionSetsActive 21: [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive 21: [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 21: [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive 21: [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) 21: [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup 21: [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) 21: [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack 21: [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) 21: [ RUN ] QMMMOptionsTest.CP2KInputProcessing 21: [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) 21: [----------] 9 tests from QMMMOptionsTest (0 ms total) 21: 21: [----------] 1 test from QMMMForceProviderTest 21: [ RUN ] QMMMForceProviderTest.CanConstructOrNot 21: [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) 21: [----------] 1 test from QMMMForceProviderTest (0 ms total) 21: 21: [----------] 1 test from QMMMTest 21: [ RUN ] QMMMTest.ForceProviderLackingInputThrows 21: [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) 21: [----------] 1 test from QMMMTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 21 tests from 5 test suites ran. (177 ms total) 21: [ PASSED ] 21 tests. 21/91 Test #21: QMMMAppliedForcesUnitTest .................... Passed 0.45 sec test 22 Start 22: ColvarsAppliedForcesUnitTest 22: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/colvars_applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/ColvarsAppliedForcesUnitTest.xml" 22: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests 22: Test timeout computed to be: 30 22: [==========] Running 16 tests from 4 test suites. 22: [----------] Global test environment set-up. 22: [----------] 1 test from ColvarsTest 22: [ RUN ] ColvarsTest.ForceProviderLackingInputThrows 22: [ OK ] ColvarsTest.ForceProviderLackingInputThrows (0 ms) 22: [----------] 1 test from ColvarsTest (0 ms total) 22: 22: [----------] 6 tests from ColvarsOptionsTest 22: [ RUN ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive 22: [ OK ] ColvarsOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputDefaultValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputDefaultValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OutputValuesWhenActive 22: [ OK ] ColvarsOptionsTest.OutputValuesWhenActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.OptionSetsActive 22: [ OK ] ColvarsOptionsTest.OptionSetsActive (0 ms) 22: [ RUN ] ColvarsOptionsTest.InternalsToKvtAndBack 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsOptionsTest_InternalsToKvtAndBack_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -1226973302 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsOptionsTest.InternalsToKvtAndBack (26 ms) 22: [ RUN ] ColvarsOptionsTest.RetrieveEdrFilename 22: [ OK ] ColvarsOptionsTest.RetrieveEdrFilename (0 ms) 22: [----------] 6 tests from ColvarsOptionsTest (27 ms total) 22: 22: [----------] 4 tests from ColvarsPreProcessorTest 22: [ RUN ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CanConstructColvarsPreProcess_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to 1240727007 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CanConstructColvarsPreProcess (2 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckValuesFourWaters 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckValuesFourWaters_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -1379934817 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckValuesFourWaters (11 ms) 22: [ RUN ] ColvarsPreProcessorTest.CheckNestedInputFiles 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_CheckNestedInputFiles_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -73 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.CheckNestedInputFiles (12 ms) 22: [ RUN ] ColvarsPreProcessorTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsPreProcessorTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -453279873 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsPreProcessorTest.WrongColvarsInput (19 ms) 22: [----------] 4 tests from ColvarsPreProcessorTest (46 ms total) 22: 22: [----------] 5 tests from ColvarsForceProviderTest 22: [ RUN ] ColvarsForceProviderTest.CanConstructOrNot 22: [ OK ] ColvarsForceProviderTest.CanConstructOrNot (0 ms) 22: [ RUN ] ColvarsForceProviderTest.SimpleInputs 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_SimpleInputs_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -361281174 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.SimpleInputs (16 ms) 22: [ RUN ] ColvarsForceProviderTest.WrongColvarsInput 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_WrongColvarsInput_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -679494660 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.WrongColvarsInput (3 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForces4water 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 21.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: NVE simulation with an initial temperature of zero: will use a Verlet 22: buffer of 10%. Check your energy drift! 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForces4water_4water.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to -170010049 22: 22: Generated 10 of the 10 non-bonded parameter combinations 22: 22: Generated 10 of the 10 1-4 parameter combinations 22: 22: Excluding 2 bonded neighbours molecule type 'SOL' 22: Analysing residue names: 22: There are: 4 Water residues 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForces4water (72 ms) 22: [ RUN ] ColvarsForceProviderTest.CalculateForcesAlanine 22: 22: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: For a correct single-point energy evaluation with nsteps = 0, use 22: continuation = yes to avoid constraining the input coordinates. 22: 22: Generating 1-4 interactions: fudge = 0.5 22: Number of degrees of freedom in T-Coupling group rest is 66.00 22: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 22: 22: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: NVE simulation: will use the initial temperature of 300.368 K for 22: determining the Verlet buffer size 22: 22: 22: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.mdp]: 22: You are using a plain Coulomb cut-off, which might produce artifacts. 22: You might want to consider using PME electrostatics. 22: 22: 22: 22: There were 3 NOTEs 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/colvars/tests/Testing/Temporary/ColvarsForceProviderTest_CalculateForcesAlanine_ala.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 22: Setting the LD random seed to 2097671862 22: 22: Generated 2211 of the 2211 non-bonded parameter combinations 22: 22: Generated 2211 of the 2211 1-4 parameter combinations 22: 22: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 22: Analysing residue names: 22: There are: 2 Protein residues 22: Analysing Protein... 22: 22: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 22: 22: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 22: 22: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 22: 22: Note that mdrun will redetermine rlist based on the actual pair-list setup 22: 22: This run will generate roughly 0 Mb of data 22: [ OK ] ColvarsForceProviderTest.CalculateForcesAlanine (56 ms) 22: [----------] 5 tests from ColvarsForceProviderTest (149 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 16 tests from 4 test suites ran. (223 ms total) 22: [ PASSED ] 16 tests. 22/91 Test #22: ColvarsAppliedForcesUnitTest ................. Passed 0.38 sec test 23 Start 23: AppliedForcesUnitTest 23: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/applied_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/AppliedForcesUnitTest.xml" 23: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/applied_forces/tests 23: Test timeout computed to be: 30 23: [==========] Running 3 tests from 1 test suite. 23: [----------] Global test environment set-up. 23: [----------] 3 tests from ElectricFieldTest 23: [ RUN ] ElectricFieldTest.Static 23: [ OK ] ElectricFieldTest.Static (0 ms) 23: [ RUN ] ElectricFieldTest.Oscillating 23: [ OK ] ElectricFieldTest.Oscillating (0 ms) 23: [ RUN ] ElectricFieldTest.Pulsed 23: [ OK ] ElectricFieldTest.Pulsed (0 ms) 23: [----------] 3 tests from ElectricFieldTest (0 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 3 tests from 1 test suite ran. (0 ms total) 23: [ PASSED ] 3 tests. 23/91 Test #23: AppliedForcesUnitTest ........................ Passed 0.16 sec test 24 Start 24: ListedForcesTest 24: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/listed_forces-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/ListedForcesTest.xml" 24: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/listed_forces/tests 24: Test timeout computed to be: 30 24: [==========] Running 132 tests from 9 test suites. 24: [----------] Global test environment set-up. 24: [----------] 24 tests from Bond/ListedForcesTest 24: [ RUN ] Bond/ListedForcesTest.Ifunc/0 24: [ OK ] Bond/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/1 24: [ OK ] Bond/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/2 24: [ OK ] Bond/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/3 24: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/4 24: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/5 24: [ OK ] Bond/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/6 24: [ OK ] Bond/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/7 24: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/8 24: [ OK ] Bond/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/9 24: [ OK ] Bond/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/10 24: [ OK ] Bond/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/11 24: [ OK ] Bond/ListedForcesTest.Ifunc/11 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/12 24: [ OK ] Bond/ListedForcesTest.Ifunc/12 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/13 24: [ OK ] Bond/ListedForcesTest.Ifunc/13 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/14 24: [ OK ] Bond/ListedForcesTest.Ifunc/14 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/15 24: [ OK ] Bond/ListedForcesTest.Ifunc/15 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/16 24: [ OK ] Bond/ListedForcesTest.Ifunc/16 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/17 24: [ OK ] Bond/ListedForcesTest.Ifunc/17 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/18 24: [ OK ] Bond/ListedForcesTest.Ifunc/18 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/19 24: [ OK ] Bond/ListedForcesTest.Ifunc/19 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/20 24: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/21 24: [ OK ] Bond/ListedForcesTest.Ifunc/21 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/22 24: [ OK ] Bond/ListedForcesTest.Ifunc/22 (0 ms) 24: [ RUN ] Bond/ListedForcesTest.Ifunc/23 24: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms) 24: [----------] 24 tests from Bond/ListedForcesTest (14 ms total) 24: 24: [----------] 33 tests from Angle/ListedForcesTest 24: [ RUN ] Angle/ListedForcesTest.Ifunc/0 24: [ OK ] Angle/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/1 24: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/2 24: [ OK ] Angle/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/3 24: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/4 24: [ OK ] Angle/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/5 24: [ OK ] Angle/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/6 24: [ OK ] Angle/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/7 24: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/8 24: [ OK ] Angle/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/9 24: [ OK ] Angle/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/10 24: [ OK ] Angle/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/11 24: [ OK ] Angle/ListedForcesTest.Ifunc/11 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/12 24: [ OK ] Angle/ListedForcesTest.Ifunc/12 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/13 24: [ OK ] Angle/ListedForcesTest.Ifunc/13 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/14 24: [ OK ] Angle/ListedForcesTest.Ifunc/14 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/15 24: [ OK ] Angle/ListedForcesTest.Ifunc/15 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/16 24: [ OK ] Angle/ListedForcesTest.Ifunc/16 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/17 24: [ OK ] Angle/ListedForcesTest.Ifunc/17 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/18 24: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/19 24: [ OK ] Angle/ListedForcesTest.Ifunc/19 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/20 24: [ OK ] Angle/ListedForcesTest.Ifunc/20 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/21 24: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/22 24: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/23 24: [ OK ] Angle/ListedForcesTest.Ifunc/23 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/24 24: [ OK ] Angle/ListedForcesTest.Ifunc/24 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/25 24: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/26 24: [ OK ] Angle/ListedForcesTest.Ifunc/26 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/27 24: [ OK ] Angle/ListedForcesTest.Ifunc/27 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/28 24: [ OK ] Angle/ListedForcesTest.Ifunc/28 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/29 24: [ OK ] Angle/ListedForcesTest.Ifunc/29 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/30 24: [ OK ] Angle/ListedForcesTest.Ifunc/30 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/31 24: [ OK ] Angle/ListedForcesTest.Ifunc/31 (0 ms) 24: [ RUN ] Angle/ListedForcesTest.Ifunc/32 24: [ OK ] Angle/ListedForcesTest.Ifunc/32 (0 ms) 24: [----------] 33 tests from Angle/ListedForcesTest (2 ms total) 24: 24: [----------] 18 tests from Dihedral/ListedForcesTest 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (16 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (0 ms) 24: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17 24: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (0 ms) 24: [----------] 18 tests from Dihedral/ListedForcesTest (17 ms total) 24: 24: [----------] 12 tests from Polarize/ListedForcesTest 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/0 24: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/1 24: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/2 24: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/3 24: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/4 24: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/5 24: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/6 24: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/7 24: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/8 24: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/9 24: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/10 24: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Polarize/ListedForcesTest.Ifunc/11 24: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms) 24: [----------] 12 tests from Polarize/ListedForcesTest (0 ms total) 24: 24: [----------] 18 tests from Restraints/ListedForcesTest 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/0 24: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/1 24: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/2 24: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/3 24: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/4 24: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/5 24: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/6 24: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/7 24: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/8 24: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/9 24: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/10 24: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/11 24: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/12 24: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/13 24: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/14 24: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/15 24: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/16 24: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (0 ms) 24: [ RUN ] Restraints/ListedForcesTest.Ifunc/17 24: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms) 24: [----------] 18 tests from Restraints/ListedForcesTest (1 ms total) 24: 24: [----------] 3 tests from BondZeroLength/ListedForcesTest 24: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/0 24: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/0 (0 ms) 24: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/1 24: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] BondZeroLength/ListedForcesTest.Ifunc/2 24: [ OK ] BondZeroLength/ListedForcesTest.Ifunc/2 (0 ms) 24: [----------] 3 tests from BondZeroLength/ListedForcesTest (0 ms total) 24: 24: [----------] 3 tests from AngleZero/ListedForcesTest 24: [ RUN ] AngleZero/ListedForcesTest.Ifunc/0 24: [ OK ] AngleZero/ListedForcesTest.Ifunc/0 (20 ms) 24: [ RUN ] AngleZero/ListedForcesTest.Ifunc/1 24: [ OK ] AngleZero/ListedForcesTest.Ifunc/1 (0 ms) 24: [ RUN ] AngleZero/ListedForcesTest.Ifunc/2 24: [ OK ] AngleZero/ListedForcesTest.Ifunc/2 (0 ms) 24: [----------] 3 tests from AngleZero/ListedForcesTest (20 ms total) 24: 24: [----------] 12 tests from 14Interaction/ListedForcesPairsTest 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/0 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/0 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/1 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/1 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/2 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/2 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/3 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/3 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/4 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/4 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/5 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/5 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/6 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/6 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/7 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/7 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/8 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/8 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/9 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/9 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/10 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/10 (0 ms) 24: [ RUN ] 14Interaction/ListedForcesPairsTest.Ifunc/11 24: [ OK ] 14Interaction/ListedForcesPairsTest.Ifunc/11 (0 ms) 24: [----------] 12 tests from 14Interaction/ListedForcesPairsTest (1 ms total) 24: 24: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/0 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/1 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/2 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/3 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/4 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/5 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/6 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/7 (0 ms) 24: [ RUN ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 24: [ OK ] PosResBasicTest/PositionRestraintsTest.BasicPosResNoFreeEnergy/8 (0 ms) 24: [----------] 9 tests from PosResBasicTest/PositionRestraintsTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 132 tests from 9 test suites ran. (60 ms total) 24: [ PASSED ] 132 tests. 24/91 Test #24: ListedForcesTest ............................. Passed 0.31 sec test 25 Start 25: NbnxmTests 25: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/nbnxm-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/NbnxmTests.xml" 25: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/nbnxm/tests 25: Test timeout computed to be: 30 25: [==========] Running 80 tests from 3 test suites. 25: [----------] Global test environment set-up. 25: [----------] 18 tests from KernelSetupTest 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeRF 25: [ OK ] KernelSetupTest.getCoulombKernelTypeRF (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeCut 25: [ OK ] KernelSetupTest.getCoulombKernelTypeCut (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeTable 25: [ OK ] KernelSetupTest.getCoulombKernelTypeTable (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeTableTwin 25: [ OK ] KernelSetupTest.getCoulombKernelTypeTableTwin (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwald 25: [ OK ] KernelSetupTest.getCoulombKernelTypeEwald (0 ms) 25: [ RUN ] KernelSetupTest.getCoulombKernelTypeEwaldTwin 25: [ OK ] KernelSetupTest.getCoulombKernelTypeEwaldTwin (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomNone (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombGeomPotShift (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBNone (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombLBPotShift (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNoneNone (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutCombNonePotShift (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutThrows 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutThrows (16 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutForceSwitch (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypePmeGeom 25: [ OK ] KernelSetupTest.getVdwKernelTypePmeGeom (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypePmeNone 25: [ OK ] KernelSetupTest.getVdwKernelTypePmeNone (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch 25: [ OK ] KernelSetupTest.getVdwKernelTypeLjCutPotSwitch (0 ms) 25: [ RUN ] KernelSetupTest.getVdwKernelTypeAllCountThrows 25: [ OK ] KernelSetupTest.getVdwKernelTypeAllCountThrows (0 ms) 25: [----------] 18 tests from KernelSetupTest (16 ms total) 25: 25: [----------] 60 tests from NbnxmKernelTest 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwCutCombNone (3 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwForceSwitch (16 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwPotSwitch (7 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombReactionField_VdwEwaldCombGeom (16 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwCutCombNone (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwForceSwitch (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwPotSwitch (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwald_VdwEwaldCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwCutCombNone (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwForceSwitch (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwPotSwitch (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwCutCombNone (19 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwForceSwitch (8 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwPotSwitch (4 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwald_VdwEwaldCombGeom (20 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombGeom (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombLB (0 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwCutCombNone (12 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwForceSwitch (4 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwPotSwitch (20 ms) 25: [ RUN ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_plain-C_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (4 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombGeom (18 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombLB (1 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwCutCombNone (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwForceSwitch (1 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwPotSwitch (14 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombReactionField_VdwEwaldCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombLB (18 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwCutCombNone (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwForceSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwPotSwitch (14 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwald_VdwEwaldCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombLB (18 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwCutCombNone (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwForceSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwPotSwitch (10 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabNo_CoulombEwaldTwin_VdwEwaldCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombGeom (22 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombLB (18 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwCutCombNone (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwForceSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwPotSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwald_VdwEwaldCombGeom (22 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombGeom (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombLB (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwCutCombNone (18 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwForceSwitch (2 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwPotSwitch (14 ms) 25: [ RUN ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom 25: [ OK ] NbnxmKernelTest.type_SIMD4xM_TabYes_CoulombEwaldTwin_VdwEwaldCombGeom (6 ms) 25: [----------] 60 tests from NbnxmKernelTest (396 ms total) 25: 25: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest 25: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 25: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/0 (0 ms) 25: [ RUN ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 25: [ OK ] WithParameters/CpuListDiagonalExclusionsTest.CheckMask/1 (0 ms) 25: [----------] 2 tests from WithParameters/CpuListDiagonalExclusionsTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 80 tests from 3 test suites ran. (413 ms total) 25: [ PASSED ] 80 tests. 25/91 Test #25: NbnxmTests ................................... Passed 0.65 sec test 26 Start 26: CommandLineUnitTests 26: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/commandline-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/CommandLineUnitTests.xml" 26: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests 26: Test timeout computed to be: 30 26: [==========] Running 60 tests from 7 test suites. 26: [----------] Global test environment set-up. 26: [----------] 3 tests from CommandLineHelpModuleTest 26: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 26: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (13 ms) 26: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 26: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 26: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 26: [ OK ] CommandLineHelpModuleTest.ExportsHelp (0 ms) 26: [----------] 3 tests from CommandLineHelpModuleTest (13 ms total) 26: 26: [----------] 7 tests from CommandLineHelpWriterTest 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 26: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 26: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 26: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 26: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 26: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues 26: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms) 26: [----------] 7 tests from CommandLineHelpWriterTest (0 ms total) 26: 26: [----------] 6 tests from CommandLineModuleManagerTest 26: [ RUN ] CommandLineModuleManagerTest.RunsModule 26: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 26: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 26: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 26: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 26: [----------] 6 tests from CommandLineModuleManagerTest (0 ms total) 26: 26: [----------] 13 tests from CommandLineParserTest 26: [ RUN ] CommandLineParserTest.HandlesSingleValues 26: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 26: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 26: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 26: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 26: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesString 26: [ OK ] CommandLineParserTest.HandlesString (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 26: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 26: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 26: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 26: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 26: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 26: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 26: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 26: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 26: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 26: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 26: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 26: [----------] 13 tests from CommandLineParserTest (0 ms total) 26: 26: [----------] 6 tests from CommandLineProgramContextTest 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 26: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 26: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 26: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 26: 26: [----------] 3 tests from OutputNamesTest 26: [ RUN ] OutputNamesTest.CanBeSuffixed 26: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms) 26: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend 26: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms) 26: [ RUN ] OutputNamesTest.CanHavePartNumberAdded 26: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms) 26: [----------] 3 tests from OutputNamesTest (0 ms total) 26: 26: [----------] 22 tests from ParseCommonArgsTest 26: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 26: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 26: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 26: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 26: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum 26: [ OK ] ParseCommonArgsTest.ParsesBooleanArgsToValuesOfSuitableEnum (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 26: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 26: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 26: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 26: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 26: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 26: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 26: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 26: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 26: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 26: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 26: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 26: Value is /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/commandline/tests/Testing/Temporary/ParseCommonArgsTest_AcceptsUnknownTrajectoryExtension.foo 26: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 26: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 26: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 26: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 26: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (4 ms) 26: [----------] 22 tests from ParseCommonArgsTest (5 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 60 tests from 7 test suites ran. (20 ms total) 26: [ PASSED ] 60 tests. 26/91 Test #26: CommandLineUnitTests ......................... Passed 0.18 sec test 27 Start 27: DomDecTests 27: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/domdec-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/DomDecTests.xml" 27: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests 27: Test timeout computed to be: 30 27: [==========] Running 9 tests from 2 test suites. 27: [----------] Global test environment set-up. 27: [----------] 7 tests from HashedMap 27: [ RUN ] HashedMap.InsertsFinds 27: [ OK ] HashedMap.InsertsFinds (0 ms) 27: [ RUN ] HashedMap.NegativeKeysWork 27: [ OK ] HashedMap.NegativeKeysWork (0 ms) 27: [ RUN ] HashedMap.InsertsErases 27: [ OK ] HashedMap.InsertsErases (0 ms) 27: [ RUN ] HashedMap.InsertsOrAssigns 27: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 27: [ RUN ] HashedMap.Clears 27: [ OK ] HashedMap.Clears (0 ms) 27: [ RUN ] HashedMap.LinkedEntries 27: [ OK ] HashedMap.LinkedEntries (0 ms) 27: [ RUN ] HashedMap.ResizesTable 27: [ OK ] HashedMap.ResizesTable (0 ms) 27: [----------] 7 tests from HashedMap (0 ms total) 27: 27: [----------] 2 tests from LocalAtomSetManager 27: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 27: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 27: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 27: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 27: [----------] 2 tests from LocalAtomSetManager (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 9 tests from 2 test suites ran. (0 ms total) 27: [ PASSED ] 9 tests. 27/91 Test #27: DomDecTests .................................. Passed 0.18 sec test 28 Start 28: DomDecMpiTests 28: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/domdec-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/DomDecMpiTests.xml" 28: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/domdec/tests 28: Test timeout computed to be: 30 28: [==========] Running 4 tests from 1 test suite. 28: [----------] Global test environment set-up. 28: [----------] 4 tests from HaloExchangeTest 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith1Pulse 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith1Pulse (23 ms) 28: [ RUN ] HaloExchangeTest.Coordinates1dHaloWith2Pulses 28: [ OK ] HaloExchangeTest.Coordinates1dHaloWith2Pulses (26 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith1PulseInEachDim (0 ms) 28: [ RUN ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 28: [ OK ] HaloExchangeTest.Coordinates2dHaloWith2PulsesInDim1 (23 ms) 28: [----------] 4 tests from HaloExchangeTest (271 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 4 tests from 1 test suite ran. (272 ms total) 28: [ PASSED ] 4 tests. 28/91 Test #28: DomDecMpiTests ............................... Passed 1.22 sec test 29 Start 29: EwaldUnitTests 29: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/ewald-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/EwaldUnitTests.xml" 29: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/ewald/tests 29: Test timeout computed to be: 30 29: [==========] Running 407 tests from 9 test suites. 29: [----------] Global test environment set-up. 29: [----------] 6 tests from SeparatePmeRanksPermittedTest 29: [ RUN ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons 29: [ OK ] SeparatePmeRanksPermittedTest.ZeroPmeDisableReasons (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.CanBeDisabled 29: [ OK ] SeparatePmeRanksPermittedTest.CanBeDisabled (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonFlag (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.OneDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.OneDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.TwoDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.TwoDisableReasonText (0 ms) 29: [ RUN ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText 29: [ OK ] SeparatePmeRanksPermittedTest.EmptyDisableReasonText (0 ms) 29: [----------] 6 tests from SeparatePmeRanksPermittedTest (0 ms total) 29: 29: [----------] 108 tests from Pme_SplineAndSpreadTest 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spline (12 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (16 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_spread (8 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spline (13 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spline (20 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_spread (13 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_1_atom_fused spline and spread (12 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_spread (14 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spline (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_spread (2 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_rect_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (14 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spline (16 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_2_atoms_fused spline and spread (8 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_3_grid_19_17_11_system_13_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_1_atom_fused spline and spread (12 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_system_13_atoms_fused spline and spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_4_grid_19_17_11_system_13_atoms_fused spline and spread (17 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spline (5 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_spread (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_system_13_atoms_fused spline and spread (29 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_1_atom_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spline (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_2_atoms_fused spline and spread (0 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spline (1 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_spread (14 ms) 29: [ RUN ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread 29: [ OK ] Pme_SplineAndSpreadTest.WorksOn_CPU_box_tric_order_5_grid_19_17_11_system_13_atoms_fused spline and spread (2 ms) 29: [----------] 108 tests from Pme_SplineAndSpreadTest (340 ms total) 29: 29: [----------] 64 tests from Pme_SolveTest 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (12 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (8 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (4 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from Pme_SolveTest (33 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldQ_SolveTest (2 ms total) 29: 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (20 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_ (24 ms) 29: [ RUN ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy 29: [ OK ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_YZX_energy (0 ms) 29: [----------] 32 tests from PmeDiffEwaldLJ_SolveTest (48 ms total) 29: 29: [----------] 64 tests from PmeDiffEps_SolveTest 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_YZX_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: ./src/gromacs/ewald/tests/pmesolvetest.cpp:265: Skipped 29: Test is being skipped because: 29: CPU PME solve does not implement XYZ grid ordering 29: 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_ (0 ms) 29: [ RUN ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy 29: [ OK ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_YZX_energy (0 ms) 29: [----------] 64 tests from PmeDiffEps_SolveTest (7 ms total) 29: 29: [----------] 72 tests from Pme_GatherTest 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_1_atom (8 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (8 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_rect_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_3_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_4_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_first_system_13_atoms (12 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_16_12_14_gridvalues_second_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_first_system_13_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_1_atom (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_2_atoms (0 ms) 29: [ RUN ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms 29: [ OK ] Pme_GatherTest.WorksOn_CPU_box_tric_order_5_grid_13_15_11_gridvalues_second_system_13_atoms (0 ms) 29: [----------] 72 tests from Pme_GatherTest (37 ms total) 29: 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (1 ms) 29: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 29: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 29: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (1 ms total) 29: 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (5 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (13 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (5 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (13 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (5 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (2 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (12 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (5 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (0 ms) 29: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 29: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (0 ms) 29: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (80 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 407 tests from 9 test suites ran. (551 ms total) 29: [ PASSED ] 311 tests. 29: [ SKIPPED ] 96 tests, listed below: 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] Pme_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldQ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_0_4_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEwaldLJ_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_2_ewaldq_2_ewaldlj_2_35_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_rect_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_16_12_28_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_first_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_Coulomb_order_XYZ_energy 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_ 29: [ SKIPPED ] PmeDiffEps_SolveTest.WorksOnCPU_box_tric_grid_9_7_23_gridvalues_second_eps_1_9_ewaldq_2_ewaldlj_0_7_LJ_order_XYZ_energy 29/91 Test #29: EwaldUnitTests ............................... Passed 0.91 sec test 30 Start 30: FFTUnitTests 30: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/fft-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/FFTUnitTests.xml" 30: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fft/tests 30: Test timeout computed to be: 1920 30: [==========] Running 15 tests from 4 test suites. 30: [----------] Global test environment set-up. 30: [----------] 2 tests from ManyFFTTest 30: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (18 ms) 30: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 30: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (4 ms) 30: [----------] 2 tests from ManyFFTTest (23 ms total) 30: 30: [----------] 1 test from FFTTest 30: [ RUN ] FFTTest.Real2DLength18_15Test 30: [ OK ] FFTTest.Real2DLength18_15Test (5 ms) 30: [----------] 1 test from FFTTest (5 ms total) 30: 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (6 ms) 30: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 30: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (19 ms) 30: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (29 ms total) 30: 30: [----------] 2 tests from Works/ParameterizedFFTTest3D 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_6_9 (0 ms) 30: [ RUN ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 30: [ OK ] Works/ParameterizedFFTTest3D.RunsOnHost/5_5_10 (0 ms) 30: [----------] 2 tests from Works/ParameterizedFFTTest3D (1 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 15 tests from 4 test suites ran. (59 ms total) 30: [ PASSED ] 15 tests. 30/91 Test #30: FFTUnitTests ................................. Passed 0.17 sec test 31 Start 31: GpuUtilsUnitTests 31: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gpu_utils-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GpuUtilsUnitTests.xml" 31: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gpu_utils/tests 31: Test timeout computed to be: 30 31: [==========] Running 64 tests from 22 test suites. 31: [----------] Global test environment set-up. 31: [----------] 2 tests from ClfftInitializer 31: [ RUN ] ClfftInitializer.SingleInitializationWorks 31: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms) 31: [ RUN ] ClfftInitializer.TwoInitializationsWork 31: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms) 31: [----------] 2 tests from ClfftInitializer (0 ms total) 31: 31: [----------] 1 test from DevicesAvailable 31: [ RUN ] DevicesAvailable.ShouldBeAbleToRunOnDevice 31: [ OK ] DevicesAvailable.ShouldBeAbleToRunOnDevice (0 ms) 31: [----------] 1 test from DevicesAvailable (0 ms total) 31: 31: [----------] 1 test from DeviceStreamManagerTest 31: [ RUN ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice 31: [ OK ] DeviceStreamManagerTest.CorrectStreamsAreReturnedOnNonbondedDevice (0 ms) 31: [----------] 1 test from DeviceStreamManagerTest (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 31: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 31: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 31: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 31: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 31: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 31: 31: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 31: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 31: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 31: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 31: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 31: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 31: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Swap 31: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/0.Comparison 31: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 31: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Swap 31: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/1.Comparison 31: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 31: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Swap 31: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/2.Comparison 31: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 31: 31: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 31: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 31: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 31: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 31: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Swap 31: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 31: [ RUN ] HostAllocatorTestNoMem/3.Comparison 31: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 31: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 31: 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 31: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 31: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 31: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 31: 31: [----------] 1 test from HostAllocatorUntypedTest 31: [ RUN ] HostAllocatorUntypedTest.Comparison 31: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 31: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/0.Move 31: [ OK ] AllocatorTest/0.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/0 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/1.Move 31: [ OK ] AllocatorTest/1.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/1 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 31: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/2.Move 31: [ OK ] AllocatorTest/2.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/2 (0 ms total) 31: 31: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 31: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 31: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 31: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 31: [ RUN ] AllocatorTest/3.Move 31: [ OK ] AllocatorTest/3.Move (0 ms) 31: [----------] 4 tests from AllocatorTest/3 (0 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 64 tests from 22 test suites ran. (0 ms total) 31: [ PASSED ] 64 tests. 31/91 Test #31: GpuUtilsUnitTests ............................ Passed 0.16 sec test 32 Start 32: HardwareUnitTests 32: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/hardware-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/HardwareUnitTests.xml" 32: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/hardware/tests 32: Test timeout computed to be: 30 32: [==========] Running 21 tests from 9 test suites. 32: [----------] Global test environment set-up. 32: [----------] 1 test from CpuInfoTest 32: [ RUN ] CpuInfoTest.SupportLevel 32: [ OK ] CpuInfoTest.SupportLevel (0 ms) 32: [----------] 1 test from CpuInfoTest (0 ms total) 32: 32: [----------] 4 tests from HardwareTopologyTest 32: [ RUN ] HardwareTopologyTest.Execute 32: [ OK ] HardwareTopologyTest.Execute (24 ms) 32: [ RUN ] HardwareTopologyTest.HwlocExecute 32: [ OK ] HardwareTopologyTest.HwlocExecute (8 ms) 32: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 32: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (19 ms) 32: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 32: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (23 ms) 32: [----------] 4 tests from HardwareTopologyTest (76 ms total) 32: 32: [----------] 1 test from DevicesManagerTest 32: [ RUN ] DevicesManagerTest.Serialization 32: [ OK ] DevicesManagerTest.Serialization (0 ms) 32: [----------] 1 test from DevicesManagerTest (0 ms total) 32: 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] XeonE52620/MockHardwareTopologyTest.DetectsHardware/4 (16 ms) 32: [----------] 5 tests from XeonE52620/MockHardwareTopologyTest (18 ms total) 32: 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/2 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/3 (0 ms) 32: [ RUN ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 32: [ OK ] Xeon4116/MockHardwareTopologyTest.DetectsHardware/4 (0 ms) 32: [----------] 5 tests from Xeon4116/MockHardwareTopologyTest (2 ms total) 32: 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/0 (0 ms) 32: [ RUN ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 32: [ OK ] Core12900K/MockHardwareTopologyTest.DetectsHardware/1 (0 ms) 32: [----------] 2 tests from Core12900K/MockHardwareTopologyTest (1 ms total) 32: 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Core12900K/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (16 ms) 32: [----------] 1 test from Core12900K/MockHardwareTopologySpecialSystemTest (17 ms total) 32: 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest 32: [ RUN ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] Power9/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (0 ms) 32: [----------] 1 test from Power9/MockHardwareTopologySpecialSystemTest (1 ms total) 32: 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest 32: [ RUN ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 32: [ OK ] A64fx/MockHardwareTopologySpecialSystemTest.DetectsHardware/0 (19 ms) 32: [----------] 1 test from A64fx/MockHardwareTopologySpecialSystemTest (19 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 21 tests from 9 test suites ran. (136 ms total) 32: [ PASSED ] 21 tests. 32/91 Test #32: HardwareUnitTests ............................ Passed 0.29 sec test 33 Start 33: MathUnitTests 33: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/math-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MathUnitTests.xml" 33: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/math/tests 33: Test timeout computed to be: 30 33: [==========] Running 304 tests from 38 test suites. 33: [----------] Global test environment set-up. 33: [----------] 1 test from EmptyArrayRefWithPaddingTest 33: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 33: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 33: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 33: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 33: 33: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 33: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 33: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 33: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 33: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 33: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 33: 33: [----------] 2 tests from InvertBoxMatrixTest 33: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 33: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 33: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 33: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 33: 33: [----------] 11 tests from TranslateAndScaleTest 33: [ RUN ] TranslateAndScaleTest.identityTransformation 33: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling 33: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation 33: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector 33: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivialSingeVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingIdentity 33: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivial 33: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingNonTrivialSingleVector 33: [ OK ] TranslateAndScaleTest.scalingNonTrivialSingleVector (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero 33: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms) 33: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector 33: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZeroSingleVector (0 ms) 33: [----------] 11 tests from TranslateAndScaleTest (0 ms total) 33: 33: [----------] 3 tests from AffineTransformationTest 33: [ RUN ] AffineTransformationTest.identityTransformYieldsSameVectors 33: [ OK ] AffineTransformationTest.identityTransformYieldsSameVectors (0 ms) 33: [ RUN ] AffineTransformationTest.applyTransformationToVectors 33: [ OK ] AffineTransformationTest.applyTransformationToVectors (0 ms) 33: [ RUN ] AffineTransformationTest.retrieveGradient 33: [ OK ] AffineTransformationTest.retrieveGradient (0 ms) 33: [----------] 3 tests from AffineTransformationTest (0 ms total) 33: 33: [----------] 14 tests from DensitySimilarityTest 33: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect 33: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch 33: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms) 33: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect 33: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero 33: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect 33: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (25 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (17 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (4 ms) 33: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect 33: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationCorrect 33: [ OK ] DensitySimilarityTest.NormalizationCorrect (0 ms) 33: [ RUN ] DensitySimilarityTest.NormalizationAllNonPositive 33: [ OK ] DensitySimilarityTest.NormalizationAllNonPositive (0 ms) 33: [----------] 14 tests from DensitySimilarityTest (48 ms total) 33: 33: [----------] 6 tests from StructureSimilarityTest 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 33: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 33: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 33: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 33: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 33: [----------] 6 tests from StructureSimilarityTest (0 ms total) 33: 33: [----------] 8 tests from ExponentialMovingAverage 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms) 33: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative 33: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms) 33: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue 33: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue 33: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms) 33: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly 33: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms) 33: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing 33: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms) 33: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect 33: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms) 33: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree 33: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms) 33: [----------] 8 tests from ExponentialMovingAverage (0 ms total) 33: 33: [----------] 21 tests from FunctionTest 33: [ RUN ] FunctionTest.StaticLog2 33: [ OK ] FunctionTest.StaticLog2 (0 ms) 33: [ RUN ] FunctionTest.Log2I32Bit 33: [ OK ] FunctionTest.Log2I32Bit (0 ms) 33: [ RUN ] FunctionTest.Log2I64Bit 33: [ OK ] FunctionTest.Log2I64Bit (0 ms) 33: [ RUN ] FunctionTest.GreatestCommonDivisor 33: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 33: [ RUN ] FunctionTest.InvsqrtFloat 33: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvsqrtDouble 33: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvsqrtInteger 33: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 33: [ RUN ] FunctionTest.InvcbrtFloat 33: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 33: [ RUN ] FunctionTest.InvcbrtDouble 33: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 33: [ RUN ] FunctionTest.InvcbrtInteger 33: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 33: [ RUN ] FunctionTest.SixthrootFloat 33: [ OK ] FunctionTest.SixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.SixthrootDouble 33: [ OK ] FunctionTest.SixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.SixthrootInteger 33: [ OK ] FunctionTest.SixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootFloat 33: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootDouble 33: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 33: [ RUN ] FunctionTest.InvsixthrootInteger 33: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 33: [ RUN ] FunctionTest.Powers 33: [ OK ] FunctionTest.Powers (0 ms) 33: [ RUN ] FunctionTest.ErfInvFloat 33: [ OK ] FunctionTest.ErfInvFloat (0 ms) 33: [ RUN ] FunctionTest.ErfInvDouble 33: [ OK ] FunctionTest.ErfInvDouble (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 33: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 33: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 33: [----------] 21 tests from FunctionTest (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/0, where TypeParam = char 33: [ RUN ] FunctionTestIntegerTypes/0.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/0.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/0 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/1, where TypeParam = unsigned char 33: [ RUN ] FunctionTestIntegerTypes/1.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/1.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/1 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/2, where TypeParam = int 33: [ RUN ] FunctionTestIntegerTypes/2.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/2.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/2 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/3, where TypeParam = unsigned int 33: [ RUN ] FunctionTestIntegerTypes/3.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/3.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/3 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/4, where TypeParam = long 33: [ RUN ] FunctionTestIntegerTypes/4.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/4.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/4 (0 ms total) 33: 33: [----------] 1 test from FunctionTestIntegerTypes/5, where TypeParam = unsigned long 33: [ RUN ] FunctionTestIntegerTypes/5.IsPowerOfTwo 33: [ OK ] FunctionTestIntegerTypes/5.IsPowerOfTwo (0 ms) 33: [----------] 1 test from FunctionTestIntegerTypes/5 (0 ms total) 33: 33: [----------] 4 tests from GaussianOn1DLattice 33: [ RUN ] GaussianOn1DLattice.sumsCloseToOne 33: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms) 33: [ RUN ] GaussianOn1DLattice.isCorrect 33: [ OK ] GaussianOn1DLattice.isCorrect (0 ms) 33: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero 33: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms) 33: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange 33: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms) 33: [----------] 4 tests from GaussianOn1DLattice (0 ms total) 33: 33: [----------] 9 tests from GaussTransformTest 33: [ RUN ] GaussTransformTest.isZeroUponConstruction 33: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss 33: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms) 33: [ RUN ] GaussTransformTest.isZeroAfterSettingZero 33: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms) 33: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ 33: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms) 33: [ RUN ] GaussTransformTest.complementaryGaussAddToZero 33: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms) 33: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues 33: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms) 33: [ RUN ] GaussTransformTest.view 33: [ OK ] GaussTransformTest.view (0 ms) 33: [----------] 9 tests from GaussTransformTest (0 ms total) 33: 33: [----------] 3 tests from DensityFittingForce 33: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity 33: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms) 33: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections 33: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms) 33: [ RUN ] DensityFittingForce.pullsTowardsDerivative 33: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms) 33: [----------] 3 tests from DensityFittingForce (0 ms total) 33: 33: [----------] 2 tests from InvertMatrixTest 33: [ RUN ] InvertMatrixTest.IdentityIsImpotent 33: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 33: [ RUN ] InvertMatrixTest.ComputesInverse 33: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 33: [----------] 2 tests from InvertMatrixTest (0 ms total) 33: 33: [----------] 17 tests from MatrixTest 33: [ RUN ] MatrixTest.canSetFromArray 33: [ OK ] MatrixTest.canSetFromArray (0 ms) 33: [ RUN ] MatrixTest.canSetStaticallyFromList 33: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms) 33: [ RUN ] MatrixTest.canConstructAndFill 33: [ OK ] MatrixTest.canConstructAndFill (0 ms) 33: [ RUN ] MatrixTest.canSetValues 33: [ OK ] MatrixTest.canSetValues (0 ms) 33: [ RUN ] MatrixTest.canCopyAssign 33: [ OK ] MatrixTest.canCopyAssign (0 ms) 33: [ RUN ] MatrixTest.canSwap 33: [ OK ] MatrixTest.canSwap (0 ms) 33: [ RUN ] MatrixTest.staticMultiDimArrayExtent 33: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MatrixTest.determinantWorks 33: [ OK ] MatrixTest.determinantWorks (0 ms) 33: [ RUN ] MatrixTest.noninvertableDeterminantIsZero 33: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms) 33: [ RUN ] MatrixTest.determinantOfDiagonalMatrix 33: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms) 33: [ RUN ] MatrixTest.traceWorks 33: [ OK ] MatrixTest.traceWorks (0 ms) 33: [ RUN ] MatrixTest.transposeWorks 33: [ OK ] MatrixTest.transposeWorks (0 ms) 33: [ RUN ] MatrixTest.transposeOfSymmetricMatrix 33: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms) 33: [ RUN ] MatrixTest.canCreateFromLegacyMatrix 33: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.canFillLegacyMatrix 33: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms) 33: [ RUN ] MatrixTest.IdentityMatrix 33: [ OK ] MatrixTest.IdentityMatrix (0 ms) 33: [ RUN ] MatrixTest.MatrixVectorMultiplication 33: [ OK ] MatrixTest.MatrixVectorMultiplication (0 ms) 33: [----------] 17 tests from MatrixTest (0 ms total) 33: 33: [----------] 25 tests from MultiDimArrayTest 33: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic 33: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic 33: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInStatic 33: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic 33: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructStatic 33: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic 33: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignStatic 33: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic 33: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructStatic 33: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic 33: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignStatic 33: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic 33: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapStatic 33: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms) 33: [ RUN ] MultiDimArrayTest.canSwapDynamic 33: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms) 33: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue 33: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms) 33: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray 33: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToView 33: [ OK ] MultiDimArrayTest.conversionToView (0 ms) 33: [ RUN ] MultiDimArrayTest.conversionToConstView 33: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms) 33: [ RUN ] MultiDimArrayTest.viewBegin 33: [ OK ] MultiDimArrayTest.viewBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.viewEnd 33: [ OK ] MultiDimArrayTest.viewEnd (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstBegin 33: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms) 33: [ RUN ] MultiDimArrayTest.constViewConstEnd 33: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms) 33: [----------] 25 tests from MultiDimArrayTest (0 ms total) 33: 33: [----------] 4 tests from MultiDimArrayToMdSpanTest 33: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms) 33: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan 33: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms) 33: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total) 33: 33: [----------] 9 tests from NelderMeadSimplexTest 33: [ RUN ] NelderMeadSimplexTest.BestVertex 33: [ OK ] NelderMeadSimplexTest.BestVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.WorstVertex 33: [ OK ] NelderMeadSimplexTest.WorstVertex (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SecondWorstValue 33: [ OK ] NelderMeadSimplexTest.SecondWorstValue (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ReflectionPoint 33: [ OK ] NelderMeadSimplexTest.ReflectionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateExpansionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateExpansionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.EvaluateContractionPoint 33: [ OK ] NelderMeadSimplexTest.EvaluateContractionPoint (0 ms) 33: [ RUN ] NelderMeadSimplexTest.SwapOutWorst 33: [ OK ] NelderMeadSimplexTest.SwapOutWorst (0 ms) 33: [ RUN ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest 33: [ OK ] NelderMeadSimplexTest.ShrinkSimplexPointsExceptBest (0 ms) 33: [ RUN ] NelderMeadSimplexTest.OrientedLength 33: [ OK ] NelderMeadSimplexTest.OrientedLength (0 ms) 33: [----------] 9 tests from NelderMeadSimplexTest (0 ms total) 33: 33: [----------] 2 tests from NelderMead 33: [ RUN ] NelderMead.Optimizes2DFunctionCorrectly 33: [ OK ] NelderMead.Optimizes2DFunctionCorrectly (19 ms) 33: [ RUN ] NelderMead.Optimizes3DFunctorCorrectly 33: [ OK ] NelderMead.Optimizes3DFunctorCorrectly (0 ms) 33: [----------] 2 tests from NelderMead (19 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/0, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/0.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/0.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ResizeWorks 33: [ OK ] PaddedVectorTest/0.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorks 33: [ OK ] PaddedVectorTest/0.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/0.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/0.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/0.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/0.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanCopyAssign 33: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanMoveAssign 33: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/0.CanSwap 33: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/0 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/1, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/1.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/1.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ResizeWorks 33: [ OK ] PaddedVectorTest/1.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorks 33: [ OK ] PaddedVectorTest/1.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/1.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/1.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/1.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/1.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanCopyAssign 33: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanMoveAssign 33: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/1.CanSwap 33: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/1 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/2, where TypeParam = std::allocator 33: [ RUN ] PaddedVectorTest/2.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/2.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ResizeWorks 33: [ OK ] PaddedVectorTest/2.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorks 33: [ OK ] PaddedVectorTest/2.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/2.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/2.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/2.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/2.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanCopyAssign 33: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanMoveAssign 33: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/2.CanSwap 33: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/2 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/3.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/3.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ResizeWorks 33: [ OK ] PaddedVectorTest/3.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorks 33: [ OK ] PaddedVectorTest/3.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/3.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/3.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/3.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/3.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanCopyAssign 33: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanMoveAssign 33: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/3.CanSwap 33: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/3 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 33: [ RUN ] PaddedVectorTest/4.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/4.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ResizeWorks 33: [ OK ] PaddedVectorTest/4.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorks 33: [ OK ] PaddedVectorTest/4.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/4.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/4.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/4.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/4.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanCopyAssign 33: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanMoveAssign 33: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/4.CanSwap 33: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/4 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/5.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/5.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ResizeWorks 33: [ OK ] PaddedVectorTest/5.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorks 33: [ OK ] PaddedVectorTest/5.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/5.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/5.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/5.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/5.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanCopyAssign 33: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanMoveAssign 33: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/5.CanSwap 33: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/5 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/6.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/6.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ResizeWorks 33: [ OK ] PaddedVectorTest/6.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorks 33: [ OK ] PaddedVectorTest/6.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/6.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/6.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/6.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/6.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanCopyAssign 33: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanMoveAssign 33: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/6.CanSwap 33: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/6 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 33: [ RUN ] PaddedVectorTest/7.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/7.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ResizeWorks 33: [ OK ] PaddedVectorTest/7.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorks 33: [ OK ] PaddedVectorTest/7.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/7.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/7.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/7.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/7.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanCopyAssign 33: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanMoveAssign 33: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/7.CanSwap 33: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/7 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/8.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/8.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ResizeWorks 33: [ OK ] PaddedVectorTest/8.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorks 33: [ OK ] PaddedVectorTest/8.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/8.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/8.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/8.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/8.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanCopyAssign 33: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanMoveAssign 33: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/8.CanSwap 33: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/8 (0 ms total) 33: 33: [----------] 11 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 33: [ RUN ] PaddedVectorTest/9.DefaultConstructorWorks 33: [ OK ] PaddedVectorTest/9.DefaultConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ResizeWorks 33: [ OK ] PaddedVectorTest/9.ResizeWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorks 33: [ OK ] PaddedVectorTest/9.ReserveWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve 33: [ OK ] PaddedVectorTest/9.ReserveWorksTheSameAsNoReserve (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks 33: [ OK ] PaddedVectorTest/9.MoveConstructorWithAllocatorWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.MoveAssignmentWorks 33: [ OK ] PaddedVectorTest/9.MoveAssignmentWorks (0 ms) 33: [ RUN ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical 33: [ OK ] PaddedVectorTest/9.ArrayRefConversionsAreIdentical (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanCopyAssign 33: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanMoveAssign 33: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 33: [ RUN ] PaddedVectorTest/9.CanSwap 33: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 33: [----------] 11 tests from PaddedVectorTest/9 (0 ms total) 33: 33: [----------] 40 tests from RVecTest 33: [ RUN ] RVecTest.CanBeStoredInVector 33: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 33: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 33: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAsMutable_rvec 33: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Array 33: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 33: [ RUN ] RVecTest.ComparesEqual 33: [ OK ] RVecTest.ComparesEqual (0 ms) 33: [ RUN ] RVecTest.ComparesUnequal 33: [ OK ] RVecTest.ComparesUnequal (0 ms) 33: [ RUN ] RVecTest.CanAddRVecToRvec 33: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanAddAssignRVecToRvec 33: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractRVecFromRvec 33: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 33: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 33: [ RUN ] RVecTest.CanDotProductRVecByRvec 33: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanCrossProductRVecByRvec 33: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVecInplace 33: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 33: [ RUN ] RVecTest.CanScaleRVec 33: [ OK ] RVecTest.CanScaleRVec (0 ms) 33: [ RUN ] RVecTest.CanDivideRVec 33: [ OK ] RVecTest.CanDivideRVec (0 ms) 33: [ RUN ] RVecTest.CanDoUnitvFromRVec 33: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanSqLengthOfRVec 33: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanLengthOfRVec 33: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToRVec 33: [ OK ] RVecTest.CanCastToRVec (0 ms) 33: [ RUN ] RVecTest.CanCastToDVec 33: [ OK ] RVecTest.CanCastToDVec (0 ms) 33: [ RUN ] RVecTest.CanLeftScalarMultiply 33: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanRightScalarMultiply 33: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 33: [ RUN ] RVecTest.CanGetUnitvFromRVec 33: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 33: [ RUN ] RVecTest.CanGetSqLengthOfRVec 33: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanGetLengthOfRVec 33: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoCrossProductOfRVec 33: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanDoDotProductOfRVec 33: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 33: [ RUN ] RVecTest.CanScaleByVector 33: [ OK ] RVecTest.CanScaleByVector (0 ms) 33: [ RUN ] RVecTest.CanNegate 33: [ OK ] RVecTest.CanNegate (0 ms) 33: [ RUN ] RVecTest.asIVec 33: [ OK ] RVecTest.asIVec (0 ms) 33: [ RUN ] RVecTest.elementWiseMin 33: [ OK ] RVecTest.elementWiseMin (0 ms) 33: [ RUN ] RVecTest.elementWiseMax 33: [ OK ] RVecTest.elementWiseMax (0 ms) 33: [ RUN ] RVecTest.WorksAs_dvec_Reference 33: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_ivec_Reference 33: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 33: [ RUN ] RVecTest.WorksAs_rvec_Reference 33: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 33: [ RUN ] RVecTest.CopyConstructorWorks 33: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 33: [ RUN ] RVecTest.CopyAssignmentWorks 33: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 33: [ RUN ] RVecTest.MoveConstructorWorks 33: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 33: [ RUN ] RVecTest.MoveAssignmentWorks 33: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 33: [----------] 40 tests from RVecTest (0 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 304 tests from 38 test suites ran. (71 ms total) 33: [ PASSED ] 304 tests. 33/91 Test #33: MathUnitTests ................................ Passed 0.21 sec test 34 Start 34: MdrunUtilityUnitTests 34: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrunutility-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 34: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests 34: Test timeout computed to be: 30 34: [==========] Running 21 tests from 2 test suites. 34: [----------] Global test environment set-up. 34: [----------] 4 tests from MDModulesNotifierTest 34: [ RUN ] MDModulesNotifierTest.AddConsumer 34: [ OK ] MDModulesNotifierTest.AddConsumer (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerWithPointerParameter 34: [ OK ] MDModulesNotifierTest.AddConsumerWithPointerParameter (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddTwoDifferentConsumers 34: [ OK ] MDModulesNotifierTest.AddTwoDifferentConsumers (0 ms) 34: [ RUN ] MDModulesNotifierTest.AddConsumerOfTwoResources 34: [ OK ] MDModulesNotifierTest.AddConsumerOfTwoResources (0 ms) 34: [----------] 4 tests from MDModulesNotifierTest (0 ms total) 34: 34: [----------] 17 tests from ThreadAffinityTest 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 34: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 34: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 34: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 34: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 34: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 34: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 34: NOTE: Affinity setting failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (22 ms) 34: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 34: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (11 ms) 34: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 34: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 34: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 34: NOTE: Affinity setting for 1/2 threads failed. 34: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 34: [----------] 17 tests from ThreadAffinityTest (36 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 21 tests from 2 test suites ran. (36 ms total) 34: [ PASSED ] 21 tests. 34/91 Test #34: MdrunUtilityUnitTests ........................ Passed 0.21 sec test 35 Start 35: MdrunUtilityMpiUnitTests 35: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 35: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdrunutility/tests 35: Test timeout computed to be: 30 35: [==========] Running 13 tests from 2 test suites. 35: [----------] Global test environment set-up. 35: [----------] 6 tests from ThreadAffinityMultiRankTest 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 35: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (104 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 35: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (116 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 35: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (126 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 35: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (107 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (119 ms) 35: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 35: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (111 ms) 35: [----------] 6 tests from ThreadAffinityMultiRankTest (863 ms total) 35: 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMainOnly (61 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMainOnly (91 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMain (143 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMainOnly (123 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMainOnly (139 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMainOnly (72 ms) 35: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly 35: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMainOnly (110 ms) 35: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (927 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 13 tests from 2 test suites ran. (1803 ms total) 35: [ PASSED ] 13 tests. 35/91 Test #35: MdrunUtilityMpiUnitTests ..................... Passed 2.74 sec test 36 Start 36: MDSpanTests 36: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdspan-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MDSpanTests.xml" 36: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdspan/tests 36: Test timeout computed to be: 30 36: [==========] Running 32 tests from 7 test suites. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from BasicAccessorPolicy 36: [ RUN ] BasicAccessorPolicy.Decay 36: [ OK ] BasicAccessorPolicy.Decay (0 ms) 36: [ RUN ] BasicAccessorPolicy.Access 36: [ OK ] BasicAccessorPolicy.Access (0 ms) 36: [ RUN ] BasicAccessorPolicy.Offset 36: [ OK ] BasicAccessorPolicy.Offset (0 ms) 36: [ RUN ] BasicAccessorPolicy.CopyAccessor 36: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms) 36: [----------] 4 tests from BasicAccessorPolicy (0 ms total) 36: 36: [----------] 4 tests from ExtentsTest 36: [ RUN ] ExtentsTest.Construction 36: [ OK ] ExtentsTest.Construction (0 ms) 36: [ RUN ] ExtentsTest.PurelyStatic 36: [ OK ] ExtentsTest.PurelyStatic (0 ms) 36: [ RUN ] ExtentsTest.RankNought 36: [ OK ] ExtentsTest.RankNought (0 ms) 36: [ RUN ] ExtentsTest.Assignment 36: [ OK ] ExtentsTest.Assignment (0 ms) 36: [----------] 4 tests from ExtentsTest (0 ms total) 36: 36: [----------] 8 tests from MdSpanExtension 36: [ RUN ] MdSpanExtension.SlicingAllStatic 36: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingDynamic 36: [ OK ] MdSpanExtension.SlicingDynamic (0 ms) 36: [ RUN ] MdSpanExtension.SlicingAllStatic3D 36: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms) 36: [ RUN ] MdSpanExtension.SlicingEqualsView3D 36: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms) 36: [ RUN ] MdSpanExtension.additionWorks 36: [ OK ] MdSpanExtension.additionWorks (0 ms) 36: [ RUN ] MdSpanExtension.subtractionWorks 36: [ OK ] MdSpanExtension.subtractionWorks (0 ms) 36: [ RUN ] MdSpanExtension.multiplicationWorks 36: [ OK ] MdSpanExtension.multiplicationWorks (0 ms) 36: [ RUN ] MdSpanExtension.divisionWorks 36: [ OK ] MdSpanExtension.divisionWorks (0 ms) 36: [----------] 8 tests from MdSpanExtension (0 ms total) 36: 36: [----------] 3 tests from LayoutTests 36: [ RUN ] LayoutTests.LayoutRightConstruction 36: [ OK ] LayoutTests.LayoutRightConstruction (0 ms) 36: [ RUN ] LayoutTests.LayoutRightProperties 36: [ OK ] LayoutTests.LayoutRightProperties (0 ms) 36: [ RUN ] LayoutTests.LayoutRightOperator 36: [ OK ] LayoutTests.LayoutRightOperator (0 ms) 36: [----------] 3 tests from LayoutTests (0 ms total) 36: 36: [----------] 1 test from MdSpanTest 36: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly 36: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms) 36: [----------] 1 test from MdSpanTest (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/0.Rank 36: [ OK ] MdSpanTest/0.Rank (0 ms) 36: [ RUN ] MdSpanTest/0.DynamicRank 36: [ OK ] MdSpanTest/0.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/0.Extents 36: [ OK ] MdSpanTest/0.Extents (0 ms) 36: [ RUN ] MdSpanTest/0.Strides 36: [ OK ] MdSpanTest/0.Strides (0 ms) 36: [ RUN ] MdSpanTest/0.Properties 36: [ OK ] MdSpanTest/0.Properties (0 ms) 36: [ RUN ] MdSpanTest/0.Operator 36: [ OK ] MdSpanTest/0.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/0 (0 ms total) 36: 36: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan, gmx::layout_right, gmx::accessor_basic > 36: [ RUN ] MdSpanTest/1.Rank 36: [ OK ] MdSpanTest/1.Rank (0 ms) 36: [ RUN ] MdSpanTest/1.DynamicRank 36: [ OK ] MdSpanTest/1.DynamicRank (0 ms) 36: [ RUN ] MdSpanTest/1.Extents 36: [ OK ] MdSpanTest/1.Extents (0 ms) 36: [ RUN ] MdSpanTest/1.Strides 36: [ OK ] MdSpanTest/1.Strides (0 ms) 36: [ RUN ] MdSpanTest/1.Properties 36: [ OK ] MdSpanTest/1.Properties (0 ms) 36: [ RUN ] MdSpanTest/1.Operator 36: [ OK ] MdSpanTest/1.Operator (0 ms) 36: [----------] 6 tests from MdSpanTest/1 (0 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 32 tests from 7 test suites ran. (0 ms total) 36: [ PASSED ] 32 tests. 36/91 Test #36: MDSpanTests .................................. Passed 0.49 sec test 37 Start 37: MdtypesUnitTest 37: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdtypes-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdtypesUnitTest.xml" 37: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/mdtypes/tests 37: Test timeout computed to be: 30 37: [==========] Running 97 tests from 7 test suites. 37: [----------] Global test environment set-up. 37: [----------] 4 tests from ForeingLambdaTermsDhdl 37: [ RUN ] ForeingLambdaTermsDhdl.RateCheckWorks 37: [ OK ] ForeingLambdaTermsDhdl.RateCheckWorks (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinear 37: [ OK ] ForeingLambdaTermsDhdl.AllLinear (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.AllLinearNegative 37: [ OK ] ForeingLambdaTermsDhdl.AllLinearNegative (0 ms) 37: [ RUN ] ForeingLambdaTermsDhdl.SeparateVdwCoul 37: [ OK ] ForeingLambdaTermsDhdl.SeparateVdwCoul (0 ms) 37: [----------] 4 tests from ForeingLambdaTermsDhdl (0 ms total) 37: 37: [----------] 4 tests from ObservablesReducerTest 37: [ RUN ] ObservablesReducerTest.CanMoveAssign 37: [ OK ] ObservablesReducerTest.CanMoveAssign (0 ms) 37: [ RUN ] ObservablesReducerTest.CanMoveConstruct 37: [ OK ] ObservablesReducerTest.CanMoveConstruct (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithNoSubscribers (0 ms) 37: [ RUN ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber 37: [ OK ] ObservablesReducerTest.CanBuildAndUseWithOneSubscriber (0 ms) 37: [----------] 4 tests from ObservablesReducerTest (0 ms total) 37: 37: [----------] 2 tests from CheckpointDataTest 37: [ RUN ] CheckpointDataTest.SingleDataTest 37: [ OK ] CheckpointDataTest.SingleDataTest (0 ms) 37: [ RUN ] CheckpointDataTest.MultiDataTest 37: [ OK ] CheckpointDataTest.MultiDataTest (2 ms) 37: [----------] 2 tests from CheckpointDataTest (2 ms total) 37: 37: [----------] 7 tests from ForceBuffers 37: [ RUN ] ForceBuffers.ConstructsUnpinned 37: [ OK ] ForceBuffers.ConstructsUnpinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsPinned 37: [ OK ] ForceBuffers.ConstructsPinned (0 ms) 37: [ RUN ] ForceBuffers.ConstructsEmpty 37: [ OK ] ForceBuffers.ConstructsEmpty (0 ms) 37: [ RUN ] ForceBuffers.ResizeWorks 37: [ OK ] ForceBuffers.ResizeWorks (0 ms) 37: [ RUN ] ForceBuffers.PaddingWorks 37: [ OK ] ForceBuffers.PaddingWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyWorks 37: [ OK ] ForceBuffers.CopyWorks (0 ms) 37: [ RUN ] ForceBuffers.CopyDoesNotPin 37: [ OK ] ForceBuffers.CopyDoesNotPin (0 ms) 37: [----------] 7 tests from ForceBuffers (0 ms total) 37: 37: [----------] 5 tests from MultipleTimeStepping 37: [ RUN ] MultipleTimeStepping.ChecksNumLevels 37: [ OK ] MultipleTimeStepping.ChecksNumLevels (0 ms) 37: [ RUN ] MultipleTimeStepping.SelectsForceGroups 37: [ OK ] MultipleTimeStepping.SelectsForceGroups (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksStepFactor 37: [ OK ] MultipleTimeStepping.ChecksStepFactor (0 ms) 37: [ RUN ] MultipleTimeStepping.ChecksPmeIsAtLastLevel 37: [ OK ] MultipleTimeStepping.ChecksPmeIsAtLastLevel (4 ms) 37: [ RUN ] MultipleTimeStepping.ChecksIntegrator 37: [ OK ] MultipleTimeStepping.ChecksIntegrator (0 ms) 37: [----------] 5 tests from MultipleTimeStepping (4 ms total) 37: 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseSimply/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseOverMultipleSteps/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWithoutAllNeedingReduction/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenASubscriberUsesEventually/numSubscribers3numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers0numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers1numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers2numRanks3 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks1 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks2 (0 ms) 37: [ RUN ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 37: [ OK ] WithVariousSubscriberCounts/ObservablesReducerIntegrationTest.CanBuildAndUseWhenAllSubscribersUseEventually/numSubscribers3numRanks3 (0 ms) 37: [----------] 60 tests from WithVariousSubscriberCounts/ObservablesReducerIntegrationTest (0 ms total) 37: 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/0 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/0 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/1 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/1 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/2 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/2 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/3 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/3 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/4 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/4 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/5 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/5 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/6 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/6 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/7 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/7 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/8 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/8 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/9 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/9 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/10 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/10 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/11 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/11 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/12 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/12 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/13 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/13 (0 ms) 37: [ RUN ] ChecksStepInterval/MtsIntervalTest.Works/14 37: [ OK ] ChecksStepInterval/MtsIntervalTest.Works/14 (0 ms) 37: [----------] 15 tests from ChecksStepInterval/MtsIntervalTest (0 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 97 tests from 7 test suites ran. (8 ms total) 37: [ PASSED ] 97 tests. 37/91 Test #37: MdtypesUnitTest .............................. Passed 0.18 sec test 38 Start 38: OnlineHelpUnitTests 38: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/onlinehelp-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/OnlineHelpUnitTests.xml" 38: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/onlinehelp/tests 38: Test timeout computed to be: 30 38: [==========] Running 22 tests from 4 test suites. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from TextTableFormatterTest 38: [ RUN ] TextTableFormatterTest.HandlesBasicCase 38: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesIndentation 38: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 38: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 38: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 38: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 38: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 38: [----------] 6 tests from TextTableFormatterTest (0 ms total) 38: 38: [----------] 3 tests from HelpManagerTest 38: [ RUN ] HelpManagerTest.HandlesRootTopic 38: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 38: [ RUN ] HelpManagerTest.HandlesSubTopics 38: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 38: [ RUN ] HelpManagerTest.HandlesInvalidTopics 38: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 38: [----------] 3 tests from HelpManagerTest (0 ms total) 38: 38: [----------] 2 tests from HelpTopicFormattingTest 38: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 38: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 38: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 38: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 38: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 38: 38: [----------] 11 tests from HelpWriterContextTest 38: [ RUN ] HelpWriterContextTest.FormatsParagraphs 38: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 38: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 38: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 38: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralText 38: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 38: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsBulletList 38: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 38: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 38: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsGridTable 38: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 38: [ RUN ] HelpWriterContextTest.FormatsTitles 38: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 38: [----------] 11 tests from HelpWriterContextTest (0 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 22 tests from 4 test suites ran. (1 ms total) 38: [ PASSED ] 22 tests. 38/91 Test #38: OnlineHelpUnitTests .......................... Passed 0.16 sec test 39 Start 39: OptionsUnitTests 39: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/options-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/OptionsUnitTests.xml" 39: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/tests 39: Test timeout computed to be: 30 39: [==========] Running 111 tests from 18 test suites. 39: [----------] Global test environment set-up. 39: [----------] 5 tests from AbstractOptionStorageTest 39: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 39: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 39: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 39: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 39: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 39: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 39: [----------] 5 tests from AbstractOptionStorageTest (0 ms total) 39: 39: [----------] 10 tests from FileNameOptionTest 39: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 39: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 39: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 39: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvValueWithoutExtension (0 ms) 39: [ RUN ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue 39: [ OK ] FileNameOptionTest.HandlesRequiredCsvOptionWithoutValue (0 ms) 39: [----------] 10 tests from FileNameOptionTest (0 ms total) 39: 39: [----------] 15 tests from FileNameOptionManagerTest 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 39: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (5 ms) 39: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 39: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 39: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 39: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 39: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 39: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 39: [----------] 15 tests from FileNameOptionManagerTest (5 ms total) 39: 39: [----------] 1 test from OptionsTest 39: [ RUN ] OptionsTest.FailsOnNonsafeStorage 39: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 39: [----------] 1 test from OptionsTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerTest 39: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 39: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 39: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 39: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMissingValue 39: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesExtraValue 39: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesGroups 39: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesSections 39: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 39: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 39: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 39: [----------] 9 tests from OptionsAssignerTest (0 ms total) 39: 39: [----------] 4 tests from OptionsAssignerBooleanTest 39: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 39: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 39: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 39: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 39: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 39: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 39: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 39: 39: [----------] 13 tests from OptionsAssignerIntegerTest 39: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 39: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 39: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 39: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 39: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 39: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 39: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 39: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 39: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 39: 39: [----------] 5 tests from OptionsAssignerDoubleTest 39: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 39: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 39: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 39: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 39: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 39: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 39: 39: [----------] 9 tests from OptionsAssignerStringTest 39: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 39: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 39: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 39: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 39: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 39: 39: [----------] 6 tests from OptionsAssignerEnumTest 39: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 39: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 39: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 39: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 39: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 39: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 39: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 39: 39: [----------] 8 tests from RepeatingOptionSectionTest 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 39: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 39: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 39: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 39: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 39: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 39: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 39: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 39: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 39: 39: [----------] 1 test from TimeUnitManagerTest 39: [ RUN ] TimeUnitManagerTest.BasicOperations 39: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 39: [----------] 1 test from TimeUnitManagerTest (0 ms total) 39: 39: [----------] 4 tests from TimeUnitBehaviorTest 39: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 39: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 39: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 39: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 39: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 39: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 39: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 39: 39: [----------] 2 tests from TreeValueSupportAssignTest 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 39: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 39: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 39: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 39: 39: [----------] 1 test from TreeValueSupportAssignErrorTest 39: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 39: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 39: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 39: 39: [----------] 5 tests from TreeValueSupportCheckTest 39: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 39: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 39: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 39: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 39: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 39: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 39: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 39: 39: [----------] 6 tests from TreeValueSupportAdjustTest 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 39: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 39: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 39: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 39: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 39: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 39: [----------] 6 tests from TreeValueSupportAdjustTest (0 ms total) 39: 39: [----------] 7 tests from TreeValueSupportTest 39: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 39: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 39: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsInt64Option 39: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsStringOption 39: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsFloatOption 39: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 39: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 39: [ RUN ] TreeValueSupportTest.SupportsEnumOption 39: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 39: [----------] 7 tests from TreeValueSupportTest (0 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 111 tests from 18 test suites ran. (8 ms total) 39: [ PASSED ] 111 tests. 39/91 Test #39: OptionsUnitTests ............................. Passed 0.12 sec test 40 Start 40: PbcutilUnitTest 40: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pbcutil-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/PbcutilUnitTest.xml" 40: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pbcutil/tests 40: Test timeout computed to be: 30 40: [==========] Running 37 tests from 5 test suites. 40: [----------] Global test environment set-up. 40: [----------] 1 test from ShiftTest 40: [ RUN ] ShiftTest.CoordinateShiftWorks 40: [ OK ] ShiftTest.CoordinateShiftWorks (0 ms) 40: [----------] 1 test from ShiftTest (0 ms total) 40: 40: [----------] 2 tests from MShift 40: [ RUN ] MShift.shiftsAndUnshifts 40: [ OK ] MShift.shiftsAndUnshifts (0 ms) 40: [ RUN ] MShift.shiftsAndUnshiftsSelf 40: [ OK ] MShift.shiftsAndUnshiftsSelf (0 ms) 40: [----------] 2 tests from MShift (0 ms total) 40: 40: [----------] 5 tests from PbcTest 40: [ RUN ] PbcTest.CalcShiftsWorks 40: [ OK ] PbcTest.CalcShiftsWorks (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxAlreadyInBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxAlreadyInBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInCubicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInCubicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox 40: [ OK ] PbcTest.PutAtomsInTriclinicBoxFromOutsideBox (0 ms) 40: [ RUN ] PbcTest.PutAtomsInBoxHandlesInf 40: [ OK ] PbcTest.PutAtomsInBoxHandlesInf (0 ms) 40: [----------] 5 tests from PbcTest (0 ms total) 40: 40: [----------] 2 tests from PbcEnumsTest 40: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms) 40: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect 40: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms) 40: [----------] 2 tests from PbcEnumsTest (0 ms total) 40: 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/0 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/1 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/2 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/3 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/4 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/5 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/6 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/7 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/8 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/9 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/10 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/11 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/12 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/13 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/14 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/15 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/16 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/17 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/18 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/19 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/20 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/21 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/22 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/23 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/24 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/25 (0 ms) 40: [ RUN ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 40: [ OK ] CorrectCoordinates/COMInPlaceTest.MatrixDefault/26 (0 ms) 40: [----------] 27 tests from CorrectCoordinates/COMInPlaceTest (3 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 37 tests from 5 test suites ran. (3 ms total) 40: [ PASSED ] 37 tests. 40/91 Test #40: PbcutilUnitTest .............................. Passed 0.36 sec test 41 Start 41: RandomUnitTests 41: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/random-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/RandomUnitTests.xml" 41: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/random/tests 41: Test timeout computed to be: 30 41: [==========] Running 44 tests from 10 test suites. 41: [----------] Global test environment set-up. 41: [----------] 4 tests from ExponentialDistributionTest 41: [ RUN ] ExponentialDistributionTest.Output 41: [ OK ] ExponentialDistributionTest.Output (0 ms) 41: [ RUN ] ExponentialDistributionTest.Logical 41: [ OK ] ExponentialDistributionTest.Logical (0 ms) 41: [ RUN ] ExponentialDistributionTest.Reset 41: [ OK ] ExponentialDistributionTest.Reset (0 ms) 41: [ RUN ] ExponentialDistributionTest.AltParam 41: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 41: 41: [----------] 4 tests from GammaDistributionTest 41: [ RUN ] GammaDistributionTest.Output 41: [ OK ] GammaDistributionTest.Output (0 ms) 41: [ RUN ] GammaDistributionTest.Logical 41: [ OK ] GammaDistributionTest.Logical (0 ms) 41: [ RUN ] GammaDistributionTest.Reset 41: [ OK ] GammaDistributionTest.Reset (0 ms) 41: [ RUN ] GammaDistributionTest.AltParam 41: [ OK ] GammaDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from GammaDistributionTest (0 ms total) 41: 41: [----------] 4 tests from NormalDistributionTest 41: [ RUN ] NormalDistributionTest.Output 41: [ OK ] NormalDistributionTest.Output (0 ms) 41: [ RUN ] NormalDistributionTest.Logical 41: [ OK ] NormalDistributionTest.Logical (0 ms) 41: [ RUN ] NormalDistributionTest.Reset 41: [ OK ] NormalDistributionTest.Reset (0 ms) 41: [ RUN ] NormalDistributionTest.AltParam 41: [ OK ] NormalDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from NormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from SeedTest 41: [ RUN ] SeedTest.makeRandomSeed 41: [ OK ] SeedTest.makeRandomSeed (0 ms) 41: [----------] 1 test from SeedTest (0 ms total) 41: 41: [----------] 6 tests from TabulatedNormalDistributionTest 41: [ RUN ] TabulatedNormalDistributionTest.Output14 41: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Output16 41: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 41: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Logical 41: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.Reset 41: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 41: [ RUN ] TabulatedNormalDistributionTest.AltParam 41: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 41: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 41: 41: [----------] 1 test from TabulatedNormalDistributionTableTest 41: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 41: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (0 ms) 41: [----------] 1 test from TabulatedNormalDistributionTableTest (0 ms total) 41: 41: [----------] 6 tests from ThreeFry2x64Test 41: [ RUN ] ThreeFry2x64Test.Logical 41: [ OK ] ThreeFry2x64Test.Logical (0 ms) 41: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 41: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 41: [ RUN ] ThreeFry2x64Test.Reseed 41: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 41: [ RUN ] ThreeFry2x64Test.Discard 41: [ OK ] ThreeFry2x64Test.Discard (0 ms) 41: [ RUN ] ThreeFry2x64Test.InvalidCounter 41: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 41: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 41: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 41: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 41: 41: [----------] 4 tests from UniformIntDistributionTest 41: [ RUN ] UniformIntDistributionTest.Output 41: [ OK ] UniformIntDistributionTest.Output (0 ms) 41: [ RUN ] UniformIntDistributionTest.Logical 41: [ OK ] UniformIntDistributionTest.Logical (0 ms) 41: [ RUN ] UniformIntDistributionTest.Reset 41: [ OK ] UniformIntDistributionTest.Reset (0 ms) 41: [ RUN ] UniformIntDistributionTest.AltParam 41: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 41: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 41: 41: [----------] 5 tests from UniformRealDistributionTest 41: [ RUN ] UniformRealDistributionTest.GenerateCanonical 41: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Output 41: [ OK ] UniformRealDistributionTest.Output (0 ms) 41: [ RUN ] UniformRealDistributionTest.Logical 41: [ OK ] UniformRealDistributionTest.Logical (0 ms) 41: [ RUN ] UniformRealDistributionTest.Reset 41: [ OK ] UniformRealDistributionTest.Reset (0 ms) 41: [ RUN ] UniformRealDistributionTest.AltParam 41: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 41: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 41: 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 41: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 41: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 41: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (0 ms total) 41: 41: [----------] Global test environment tear-down 41: [==========] 44 tests from 10 test suites ran. (1 ms total) 41: [ PASSED ] 44 tests. 41/91 Test #41: RandomUnitTests .............................. Passed 0.13 sec test 42 Start 42: RestraintTests 42: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/restraintpotential-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/RestraintTests.xml" 42: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/restraint/tests 42: Test timeout computed to be: 30 42: [==========] Running 1 test from 1 test suite. 42: [----------] Global test environment set-up. 42: [----------] 1 test from RestraintManager 42: [ RUN ] RestraintManager.restraintList 42: [ OK ] RestraintManager.restraintList (0 ms) 42: [----------] 1 test from RestraintManager (0 ms total) 42: 42: [----------] Global test environment tear-down 42: [==========] 1 test from 1 test suite ran. (0 ms total) 42: [ PASSED ] 1 test. 42/91 Test #42: RestraintTests ............................... Passed 0.11 sec test 43 Start 43: TableUnitTests 43: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/table-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TableUnitTests.xml" 43: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tables/tests 43: Test timeout computed to be: 30 43: [==========] Running 20 tests from 2 test suites. 43: [----------] Global test environment set-up. 43: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 43: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectInput (0 ms) 43: [ RUN ] SplineTableTest/0.Sinc 43: [ OK ] SplineTableTest/0.Sinc (0 ms) 43: [ RUN ] SplineTableTest/0.LJ12 43: [ OK ] SplineTableTest/0.LJ12 (9 ms) 43: [ RUN ] SplineTableTest/0.PmeCorrection 43: [ OK ] SplineTableTest/0.PmeCorrection (0 ms) 43: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (0 ms) 43: [ RUN ] SplineTableTest/0.TwoFunctions 43: [ OK ] SplineTableTest/0.TwoFunctions (37 ms) 43: [ RUN ] SplineTableTest/0.ThreeFunctions 43: [ OK ] SplineTableTest/0.ThreeFunctions (26 ms) 43: [ RUN ] SplineTableTest/0.Simd 43: [ OK ] SplineTableTest/0.Simd (14 ms) 43: [ RUN ] SplineTableTest/0.SimdTwoFunctions 43: [ OK ] SplineTableTest/0.SimdTwoFunctions (25 ms) 43: [----------] 10 tests from SplineTableTest/0 (114 ms total) 43: 43: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 43: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectInput (0 ms) 43: [ RUN ] SplineTableTest/1.Sinc 43: [ OK ] SplineTableTest/1.Sinc (0 ms) 43: [ RUN ] SplineTableTest/1.LJ12 43: [ OK ] SplineTableTest/1.LJ12 (0 ms) 43: [ RUN ] SplineTableTest/1.PmeCorrection 43: [ OK ] SplineTableTest/1.PmeCorrection (0 ms) 43: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 43: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 43: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 43: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (4 ms) 43: [ RUN ] SplineTableTest/1.TwoFunctions 43: [ OK ] SplineTableTest/1.TwoFunctions (1 ms) 43: [ RUN ] SplineTableTest/1.ThreeFunctions 43: [ OK ] SplineTableTest/1.ThreeFunctions (1 ms) 43: [ RUN ] SplineTableTest/1.Simd 43: [ OK ] SplineTableTest/1.Simd (0 ms) 43: [ RUN ] SplineTableTest/1.SimdTwoFunctions 43: [ OK ] SplineTableTest/1.SimdTwoFunctions (13 ms) 43: [----------] 10 tests from SplineTableTest/1 (22 ms total) 43: 43: [----------] Global test environment tear-down 43: [==========] 20 tests from 2 test suites ran. (137 ms total) 43: [ PASSED ] 20 tests. 43/91 Test #43: TableUnitTests ............................... Passed 0.27 sec test 44 Start 44: TaskAssignmentUnitTests 44: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/taskassignment-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 44: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/tests 44: Test timeout computed to be: 30 44: [==========] Running 3 tests from 2 test suites. 44: [----------] Global test environment set-up. 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest 44: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork 44: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (0 ms) 44: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid 44: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms) 44: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (0 ms total) 44: 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest 44: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow 44: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (4 ms) 44: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (4 ms total) 44: 44: [----------] Global test environment tear-down 44: [==========] 3 tests from 2 test suites ran. (4 ms total) 44: [ PASSED ] 3 tests. 44/91 Test #44: TaskAssignmentUnitTests ...................... Passed 0.16 sec test 45 Start 45: GmxTimingTests 45: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/timing-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxTimingTests.xml" 45: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/timing/tests 45: Test timeout computed to be: 30 45: [==========] Running 6 tests from 1 test suite. 45: [----------] Global test environment set-up. 45: [----------] 6 tests from TimingTest 45: [ RUN ] TimingTest.ElementCountingWorks 45: [ OK ] TimingTest.ElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.ElementNoCountingWorks 45: [ OK ] TimingTest.ElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementCountingWorks 45: [ OK ] TimingTest.SubElementCountingWorks (0 ms) 45: [ RUN ] TimingTest.SubElementNoCountingWorks 45: [ OK ] TimingTest.SubElementNoCountingWorks (0 ms) 45: [ RUN ] TimingTest.RunWallCycle 45: [ OK ] TimingTest.RunWallCycle (5 ms) 45: [ RUN ] TimingTest.RunWallCycleSub 45: [ OK ] TimingTest.RunWallCycleSub (0 ms) 45: [----------] 6 tests from TimingTest (5 ms total) 45: 45: [----------] Global test environment tear-down 45: [==========] 6 tests from 1 test suite ran. (5 ms total) 45: [ PASSED ] 6 tests. 45/91 Test #45: GmxTimingTests ............................... Passed 0.33 sec test 46 Start 46: TopologyTest 46: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/topology-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TopologyTest.xml" 46: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/topology/tests 46: Test timeout computed to be: 30 46: [==========] Running 153 tests from 10 test suites. 46: [----------] Global test environment set-up. 46: [----------] 3 tests from PdbAtomEntryTest 46: [ RUN ] PdbAtomEntryTest.CanCreateBasicEntry 46: [ OK ] PdbAtomEntryTest.CanCreateBasicEntry (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac 46: [ OK ] PdbAtomEntryTest.CanCreateEntryWithOccupAndBfac (0 ms) 46: [ RUN ] PdbAtomEntryTest.CanCreateFullEntry 46: [ OK ] PdbAtomEntryTest.CanCreateFullEntry (0 ms) 46: [----------] 3 tests from PdbAtomEntryTest (0 ms total) 46: 46: [----------] 3 tests from ExclusionBlockTest 46: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks 46: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms) 46: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka 46: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms) 46: [ RUN ] ExclusionBlockTest.MergeExclusions 46: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms) 46: [----------] 3 tests from ExclusionBlockTest (0 ms total) 46: 46: [----------] 6 tests from InteractionListTest 46: [ RUN ] InteractionListTest.EmptyWorks 46: [ OK ] InteractionListTest.EmptyWorks (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArray 46: [ OK ] InteractionListTest.CanAddInteractionArray (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionArrayMultipleAtoms 46: [ OK ] InteractionListTest.CanAddInteractionArrayMultipleAtoms (0 ms) 46: [ RUN ] InteractionListTest.CanAddInteractionPointer 46: [ OK ] InteractionListTest.CanAddInteractionPointer (0 ms) 46: [ RUN ] InteractionListTest.CanAddListToOtherList 46: [ OK ] InteractionListTest.CanAddListToOtherList (0 ms) 46: [ RUN ] InteractionListTest.ClearingWorks 46: [ OK ] InteractionListTest.ClearingWorks (0 ms) 46: [----------] 6 tests from InteractionListTest (0 ms total) 46: 46: [----------] 3 tests from IndexTest 46: [ RUN ] IndexTest.AnalyseWorksDefaultGroups 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.AnalyseWorksDefaultGroups (2 ms) 46: [ RUN ] IndexTest.WriteIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteIndexWorks (5 ms) 46: [ RUN ] IndexTest.WriteAndReadIndexWorks 46: 46: WARNING: Masses and atomic (Van der Waals) radii will be guessed 46: based on residue and atom names, since they could not be 46: definitively assigned from the information in your input 46: files. These guessed numbers might deviate from the mass 46: and radius of the atom type. Please check the output 46: files if necessary. Note, that this functionality may 46: be removed in a future GROMACS version. Please, consider 46: using another file format for your input. 46: 46: [ OK ] IndexTest.WriteAndReadIndexWorks (1 ms) 46: [----------] 3 tests from IndexTest (10 ms total) 46: 46: [----------] 4 tests from MtopTest 46: [ RUN ] MtopTest.RangeBasedLoop 46: [ OK ] MtopTest.RangeBasedLoop (0 ms) 46: [ RUN ] MtopTest.Operators 46: [ OK ] MtopTest.Operators (0 ms) 46: [ RUN ] MtopTest.CanFindResidueStartAndEndAtoms 46: [ OK ] MtopTest.CanFindResidueStartAndEndAtoms (0 ms) 46: [ RUN ] MtopTest.CanSortPerturbedInteractionsCorrectly 46: [ OK ] MtopTest.CanSortPerturbedInteractionsCorrectly (0 ms) 46: [----------] 4 tests from MtopTest (0 ms total) 46: 46: [----------] 2 tests from IListRangeTest 46: [ RUN ] IListRangeTest.RangeBasedLoopWorks 46: [ OK ] IListRangeTest.RangeBasedLoopWorks (0 ms) 46: [ RUN ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction 46: [ OK ] IListRangeTest.RangeBasedLoopWithIntermolecularInteraction (0 ms) 46: [----------] 2 tests from IListRangeTest (0 ms total) 46: 46: [----------] 13 tests from StringTableTest 46: [ RUN ] StringTableTest.AddSingleEntry 46: [ OK ] StringTableTest.AddSingleEntry (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithAt 46: [ OK ] StringTableTest.CanAccessWithAt (0 ms) 46: [ RUN ] StringTableTest.CanAccessWithBracket 46: [ OK ] StringTableTest.CanAccessWithBracket (0 ms) 46: [ RUN ] StringTableTest.ThrowsOutOfRange 46: [ OK ] StringTableTest.ThrowsOutOfRange (0 ms) 46: [ RUN ] StringTableTest.StringCompareIsCorrect 46: [ OK ] StringTableTest.StringCompareIsCorrect (0 ms) 46: [ RUN ] StringTableTest.AddTwoDistinctEntries 46: [ OK ] StringTableTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] StringTableTest.TryToAddDuplicates 46: [ OK ] StringTableTest.TryToAddDuplicates (0 ms) 46: [ RUN ] StringTableTest.AddLargeNumberOfEntries 46: [ OK ] StringTableTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] StringTableTest.NoDuplicatesInLargeTable 46: [ OK ] StringTableTest.NoDuplicatesInLargeTable (0 ms) 46: [ RUN ] StringTableTest.CanWriteToBuffer 46: [ OK ] StringTableTest.CanWriteToBuffer (0 ms) 46: [ RUN ] StringTableTest.Roundtrip 46: [ OK ] StringTableTest.Roundtrip (0 ms) 46: [ RUN ] StringTableTest.RoundtripWithCorrectStringIndices 46: [ OK ] StringTableTest.RoundtripWithCorrectStringIndices (0 ms) 46: [ RUN ] StringTableTest.CanCopyToLegacyTable 46: [ OK ] StringTableTest.CanCopyToLegacyTable (0 ms) 46: [----------] 13 tests from StringTableTest (0 ms total) 46: 46: [----------] 6 tests from LegacySymtabTest 46: [ RUN ] LegacySymtabTest.EmptyOnOpen 46: [ OK ] LegacySymtabTest.EmptyOnOpen (0 ms) 46: [ RUN ] LegacySymtabTest.AddSingleEntry 46: [ OK ] LegacySymtabTest.AddSingleEntry (0 ms) 46: [ RUN ] LegacySymtabTest.AddTwoDistinctEntries 46: [ OK ] LegacySymtabTest.AddTwoDistinctEntries (0 ms) 46: [ RUN ] LegacySymtabTest.TryToAddDuplicates 46: [ OK ] LegacySymtabTest.TryToAddDuplicates (0 ms) 46: [ RUN ] LegacySymtabTest.AddLargeNumberOfEntries 46: [ OK ] LegacySymtabTest.AddLargeNumberOfEntries (0 ms) 46: [ RUN ] LegacySymtabTest.NoDuplicatesInLargeTable 46: [ OK ] LegacySymtabTest.NoDuplicatesInLargeTable (0 ms) 46: [----------] 6 tests from LegacySymtabTest (0 ms total) 46: 46: [----------] 5 tests from TopSortTest 46: [ RUN ] TopSortTest.WorksOnEmptyIdef 46: [ OK ] TopSortTest.WorksOnEmptyIdef (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction 46: [ OK ] TopSortTest.WorksOnIdefWithNoPerturbedInteraction (0 ms) 46: [ RUN ] TopSortTest.WorksOnIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.WorksOnIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsIdefWithPerturbedInteractions (0 ms) 46: [ RUN ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions 46: [ OK ] TopSortTest.SortsMoreComplexIdefWithPerturbedInteractions (0 ms) 46: [----------] 5 tests from TopSortTest (0 ms total) 46: 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/9 (20 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanCreate/53 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/0 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/1 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/2 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/3 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/4 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/5 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/6 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/7 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/8 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/9 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/10 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/11 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/12 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/13 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/14 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/15 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/16 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/17 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/18 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/19 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/20 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/21 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/22 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/23 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/24 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/25 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/26 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/27 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/28 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/29 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/30 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/31 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/32 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/33 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/34 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/35 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/36 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/37 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/38 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/39 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/40 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/41 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/42 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/43 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/44 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/45 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/46 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/47 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/48 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/49 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/50 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/51 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/52 (0 ms) 46: [ RUN ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 46: [ OK ] BuildsValidDataStructure/SimulationParticleTest.CanSerialize/53 (0 ms) 46: [----------] 108 tests from BuildsValidDataStructure/SimulationParticleTest (25 ms total) 46: 46: [----------] Global test environment tear-down 46: [==========] 153 tests from 10 test suites ran. (37 ms total) 46: [ PASSED ] 153 tests. 46: 46: YOU HAVE 1 DISABLED TEST 46: 46/91 Test #46: TopologyTest ................................. Passed 0.21 sec test 47 Start 47: PullTest 47: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pull-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/PullTest.xml" 47: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/tests 47: Test timeout computed to be: 30 47: [==========] Running 10 tests from 1 test suite. 47: [----------] Global test environment set-up. 47: [----------] 10 tests from PullTest 47: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 47: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 47: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 47: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 47: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 47: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 47: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 47: [ RUN ] PullTest.TransformationCoordSimple 47: [ OK ] PullTest.TransformationCoordSimple (0 ms) 47: [ RUN ] PullTest.TransformationCoordAdvanced 47: [ OK ] PullTest.TransformationCoordAdvanced (0 ms) 47: [ RUN ] PullTest.TransformationCoordTime 47: [ OK ] PullTest.TransformationCoordTime (0 ms) 47: [ RUN ] PullTest.TransformationCoordTimeNotAllowed 47: [ OK ] PullTest.TransformationCoordTimeNotAllowed (0 ms) 47: [ RUN ] PullTest.TransformationCoordDummyExpression 47: [ OK ] PullTest.TransformationCoordDummyExpression (0 ms) 47: [----------] 10 tests from PullTest (0 ms total) 47: 47: [----------] Global test environment tear-down 47: [==========] 10 tests from 1 test suite ran. (0 ms total) 47: [ PASSED ] 10 tests. 47/91 Test #47: PullTest ..................................... Passed 0.12 sec test 48 Start 48: SimdUnitTests 48: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/simd-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/SimdUnitTests.xml" 48: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/simd/tests 48: Test timeout computed to be: 30 48: [==========] Running 288 tests from 22 test suites. 48: [----------] Global test environment set-up. 48: [----------] 9 tests from SimdBootstrapTest 48: [ RUN ] SimdBootstrapTest.loadStore 48: [ OK ] SimdBootstrapTest.loadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.loadU 48: [ OK ] SimdBootstrapTest.loadU (0 ms) 48: [ RUN ] SimdBootstrapTest.storeU 48: [ OK ] SimdBootstrapTest.storeU (0 ms) 48: [ RUN ] SimdBootstrapTest.loadStoreI 48: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 48: [ RUN ] SimdBootstrapTest.loadUI 48: [ OK ] SimdBootstrapTest.loadUI (0 ms) 48: [ RUN ] SimdBootstrapTest.storeUI 48: [ OK ] SimdBootstrapTest.storeUI (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4LoadStore 48: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4LoadU 48: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 48: [ RUN ] SimdBootstrapTest.simd4StoreU 48: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 48: [----------] 9 tests from SimdBootstrapTest (0 ms total) 48: 48: [----------] 41 tests from SimdScalarTest 48: [ RUN ] SimdScalarTest.load 48: [ OK ] SimdScalarTest.load (0 ms) 48: [ RUN ] SimdScalarTest.loadU 48: [ OK ] SimdScalarTest.loadU (0 ms) 48: [ RUN ] SimdScalarTest.store 48: [ OK ] SimdScalarTest.store (0 ms) 48: [ RUN ] SimdScalarTest.storeU 48: [ OK ] SimdScalarTest.storeU (0 ms) 48: [ RUN ] SimdScalarTest.setZero 48: [ OK ] SimdScalarTest.setZero (0 ms) 48: [ RUN ] SimdScalarTest.andNot 48: [ OK ] SimdScalarTest.andNot (0 ms) 48: [ RUN ] SimdScalarTest.fma 48: [ OK ] SimdScalarTest.fma (0 ms) 48: [ RUN ] SimdScalarTest.fms 48: [ OK ] SimdScalarTest.fms (0 ms) 48: [ RUN ] SimdScalarTest.fnma 48: [ OK ] SimdScalarTest.fnma (0 ms) 48: [ RUN ] SimdScalarTest.fnms 48: [ OK ] SimdScalarTest.fnms (0 ms) 48: [ RUN ] SimdScalarTest.maskAdd 48: [ OK ] SimdScalarTest.maskAdd (0 ms) 48: [ RUN ] SimdScalarTest.maskzMul 48: [ OK ] SimdScalarTest.maskzMul (0 ms) 48: [ RUN ] SimdScalarTest.maskzFma 48: [ OK ] SimdScalarTest.maskzFma (0 ms) 48: [ RUN ] SimdScalarTest.abs 48: [ OK ] SimdScalarTest.abs (0 ms) 48: [ RUN ] SimdScalarTest.max 48: [ OK ] SimdScalarTest.max (0 ms) 48: [ RUN ] SimdScalarTest.min 48: [ OK ] SimdScalarTest.min (0 ms) 48: [ RUN ] SimdScalarTest.round 48: [ OK ] SimdScalarTest.round (0 ms) 48: [ RUN ] SimdScalarTest.trunc 48: [ OK ] SimdScalarTest.trunc (0 ms) 48: [ RUN ] SimdScalarTest.reduce 48: [ OK ] SimdScalarTest.reduce (0 ms) 48: [ RUN ] SimdScalarTest.testBits 48: [ OK ] SimdScalarTest.testBits (0 ms) 48: [ RUN ] SimdScalarTest.anyTrue 48: [ OK ] SimdScalarTest.anyTrue (0 ms) 48: [ RUN ] SimdScalarTest.selectByMask 48: [ OK ] SimdScalarTest.selectByMask (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMask 48: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 48: [ RUN ] SimdScalarTest.blend 48: [ OK ] SimdScalarTest.blend (0 ms) 48: [ RUN ] SimdScalarTest.cvtR2I 48: [ OK ] SimdScalarTest.cvtR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvttR2I 48: [ OK ] SimdScalarTest.cvttR2I (0 ms) 48: [ RUN ] SimdScalarTest.cvtI2R 48: [ OK ] SimdScalarTest.cvtI2R (0 ms) 48: [ RUN ] SimdScalarTest.cvtF2D 48: [ OK ] SimdScalarTest.cvtF2D (0 ms) 48: [ RUN ] SimdScalarTest.cvtD2D 48: [ OK ] SimdScalarTest.cvtD2D (0 ms) 48: [ RUN ] SimdScalarTest.loadI 48: [ OK ] SimdScalarTest.loadI (0 ms) 48: [ RUN ] SimdScalarTest.loadUI 48: [ OK ] SimdScalarTest.loadUI (0 ms) 48: [ RUN ] SimdScalarTest.storeI 48: [ OK ] SimdScalarTest.storeI (0 ms) 48: [ RUN ] SimdScalarTest.storeUI 48: [ OK ] SimdScalarTest.storeUI (0 ms) 48: [ RUN ] SimdScalarTest.andNotI 48: [ OK ] SimdScalarTest.andNotI (0 ms) 48: [ RUN ] SimdScalarTest.testBitsI 48: [ OK ] SimdScalarTest.testBitsI (0 ms) 48: [ RUN ] SimdScalarTest.selectByMaskI 48: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 48: [ RUN ] SimdScalarTest.selectByNotMaskI 48: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 48: [ RUN ] SimdScalarTest.blendI 48: [ OK ] SimdScalarTest.blendI (0 ms) 48: [ RUN ] SimdScalarTest.cvtB2IB 48: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 48: [ RUN ] SimdScalarTest.cvtIB2B 48: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 48: [ RUN ] SimdScalarTest.expandScalarsToTriplets 48: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 48: [----------] 41 tests from SimdScalarTest (0 ms total) 48: 48: [----------] 8 tests from SimdScalarUtilTest 48: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 48: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 48: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 48: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 48: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 48: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 48: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 48: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 48: 48: [----------] 37 tests from SimdScalarMathTest 48: [ RUN ] SimdScalarMathTest.copysign 48: [ OK ] SimdScalarMathTest.copysign (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPair 48: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdScalarMathTest.inv 48: [ OK ] SimdScalarMathTest.inv (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrt 48: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdScalarMathTest.log 48: [ OK ] SimdScalarMathTest.log (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2 48: [ OK ] SimdScalarMathTest.exp2 (0 ms) 48: [ RUN ] SimdScalarMathTest.exp 48: [ OK ] SimdScalarMathTest.exp (0 ms) 48: [ RUN ] SimdScalarMathTest.erf 48: [ OK ] SimdScalarMathTest.erf (0 ms) 48: [ RUN ] SimdScalarMathTest.erfc 48: [ OK ] SimdScalarMathTest.erfc (0 ms) 48: [ RUN ] SimdScalarMathTest.sincos 48: [ OK ] SimdScalarMathTest.sincos (0 ms) 48: [ RUN ] SimdScalarMathTest.sin 48: [ OK ] SimdScalarMathTest.sin (0 ms) 48: [ RUN ] SimdScalarMathTest.cos 48: [ OK ] SimdScalarMathTest.cos (0 ms) 48: [ RUN ] SimdScalarMathTest.tan 48: [ OK ] SimdScalarMathTest.tan (0 ms) 48: [ RUN ] SimdScalarMathTest.asin 48: [ OK ] SimdScalarMathTest.asin (0 ms) 48: [ RUN ] SimdScalarMathTest.acos 48: [ OK ] SimdScalarMathTest.acos (0 ms) 48: [ RUN ] SimdScalarMathTest.atan 48: [ OK ] SimdScalarMathTest.atan (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2 48: [ OK ] SimdScalarMathTest.atan2 (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrection 48: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 48: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 48: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.invSingleAccuracy 48: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 48: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.logSingleAccuracy 48: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 48: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.expSingleAccuracy 48: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 48: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 48: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 48: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 48: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 48: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 48: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 48: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 48: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 48: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 37 tests from SimdScalarMathTest (0 ms total) 48: 48: [----------] 1 test from SimdTest 48: [ RUN ] SimdTest.GmxAligned 48: [ OK ] SimdTest.GmxAligned (0 ms) 48: [----------] 1 test from SimdTest (0 ms total) 48: 48: [----------] 42 tests from SimdFloatingpointTest 48: [ RUN ] SimdFloatingpointTest.setZero 48: [ OK ] SimdFloatingpointTest.setZero (0 ms) 48: [ RUN ] SimdFloatingpointTest.set 48: [ OK ] SimdFloatingpointTest.set (0 ms) 48: [ RUN ] SimdFloatingpointTest.add 48: [ OK ] SimdFloatingpointTest.add (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskAdd 48: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 48: [ RUN ] SimdFloatingpointTest.sub 48: [ OK ] SimdFloatingpointTest.sub (0 ms) 48: [ RUN ] SimdFloatingpointTest.mul 48: [ OK ] SimdFloatingpointTest.mul (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzMul 48: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 48: [ RUN ] SimdFloatingpointTest.fma 48: [ OK ] SimdFloatingpointTest.fma (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzFma 48: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fms 48: [ OK ] SimdFloatingpointTest.fms (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnma 48: [ OK ] SimdFloatingpointTest.fnma (0 ms) 48: [ RUN ] SimdFloatingpointTest.fnms 48: [ OK ] SimdFloatingpointTest.fnms (0 ms) 48: [ RUN ] SimdFloatingpointTest.abs 48: [ OK ] SimdFloatingpointTest.abs (0 ms) 48: [ RUN ] SimdFloatingpointTest.neg 48: [ OK ] SimdFloatingpointTest.neg (0 ms) 48: [ RUN ] SimdFloatingpointTest.and 48: [ OK ] SimdFloatingpointTest.and (0 ms) 48: [ RUN ] SimdFloatingpointTest.or 48: [ OK ] SimdFloatingpointTest.or (0 ms) 48: [ RUN ] SimdFloatingpointTest.xor 48: [ OK ] SimdFloatingpointTest.xor (0 ms) 48: [ RUN ] SimdFloatingpointTest.andNot 48: [ OK ] SimdFloatingpointTest.andNot (0 ms) 48: [ RUN ] SimdFloatingpointTest.max 48: [ OK ] SimdFloatingpointTest.max (0 ms) 48: [ RUN ] SimdFloatingpointTest.min 48: [ OK ] SimdFloatingpointTest.min (0 ms) 48: [ RUN ] SimdFloatingpointTest.round 48: [ OK ] SimdFloatingpointTest.round (0 ms) 48: [ RUN ] SimdFloatingpointTest.roundMode 48: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 48: [ RUN ] SimdFloatingpointTest.trunc 48: [ OK ] SimdFloatingpointTest.trunc (0 ms) 48: [ RUN ] SimdFloatingpointTest.frexp 48: [ OK ] SimdFloatingpointTest.frexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.ldexp 48: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 48: [ RUN ] SimdFloatingpointTest.rsqrt 48: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRsqrt 48: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 48: [ RUN ] SimdFloatingpointTest.rcp 48: [ OK ] SimdFloatingpointTest.rcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.maskzRcp 48: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.selectByNotMask 48: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpNe 48: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLe 48: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 48: [ RUN ] SimdFloatingpointTest.cmpLt 48: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 48: [ RUN ] SimdFloatingpointTest.testBits 48: [ OK ] SimdFloatingpointTest.testBits (0 ms) 48: [ RUN ] SimdFloatingpointTest.andB 48: [ OK ] SimdFloatingpointTest.andB (0 ms) 48: [ RUN ] SimdFloatingpointTest.orB 48: [ OK ] SimdFloatingpointTest.orB (0 ms) 48: [ RUN ] SimdFloatingpointTest.anyTrueB 48: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 48: [ RUN ] SimdFloatingpointTest.blend 48: [ OK ] SimdFloatingpointTest.blend (0 ms) 48: [ RUN ] SimdFloatingpointTest.reduce 48: [ OK ] SimdFloatingpointTest.reduce (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 48: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 48: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 48: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 48: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 48: 48: [----------] 16 tests from SimdFloatingpointUtilTest 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 48: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 48: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 48: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 48: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 48: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 48: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 48: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 48: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 48: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 48: 48: [----------] 23 tests from SimdIntegerTest 48: [ RUN ] SimdIntegerTest.setZero 48: [ OK ] SimdIntegerTest.setZero (0 ms) 48: [ RUN ] SimdIntegerTest.set 48: [ OK ] SimdIntegerTest.set (0 ms) 48: [ RUN ] SimdIntegerTest.add 48: [ OK ] SimdIntegerTest.add (0 ms) 48: [ RUN ] SimdIntegerTest.sub 48: [ OK ] SimdIntegerTest.sub (0 ms) 48: [ RUN ] SimdIntegerTest.mul 48: [ OK ] SimdIntegerTest.mul (0 ms) 48: [ RUN ] SimdIntegerTest.and 48: [ OK ] SimdIntegerTest.and (0 ms) 48: [ RUN ] SimdIntegerTest.andNot 48: [ OK ] SimdIntegerTest.andNot (0 ms) 48: [ RUN ] SimdIntegerTest.or 48: [ OK ] SimdIntegerTest.or (0 ms) 48: [ RUN ] SimdIntegerTest.xor 48: [ OK ] SimdIntegerTest.xor (0 ms) 48: [ RUN ] SimdIntegerTest.extract 48: [ OK ] SimdIntegerTest.extract (0 ms) 48: [ RUN ] SimdIntegerTest.cvtR2I 48: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvttR2I 48: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 48: [ RUN ] SimdIntegerTest.cvtI2R 48: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 48: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 48: [ RUN ] SimdIntegerTest.cmpLt 48: [ OK ] SimdIntegerTest.cmpLt (0 ms) 48: [ RUN ] SimdIntegerTest.testBits 48: [ OK ] SimdIntegerTest.testBits (0 ms) 48: [ RUN ] SimdIntegerTest.andB 48: [ OK ] SimdIntegerTest.andB (0 ms) 48: [ RUN ] SimdIntegerTest.orB 48: [ OK ] SimdIntegerTest.orB (0 ms) 48: [ RUN ] SimdIntegerTest.anyTrue 48: [ OK ] SimdIntegerTest.anyTrue (0 ms) 48: [ RUN ] SimdIntegerTest.blend 48: [ OK ] SimdIntegerTest.blend (0 ms) 48: [ RUN ] SimdIntegerTest.cvtB2IB 48: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 48: [ RUN ] SimdIntegerTest.cvtIB2B 48: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 48: [----------] 23 tests from SimdIntegerTest (0 ms total) 48: 48: [----------] 56 tests from SimdMathTest 48: [ RUN ] SimdMathTest.generateTestPointsFloat 48: [ OK ] SimdMathTest.generateTestPointsFloat (0 ms) 48: [ RUN ] SimdMathTest.copysign 48: [ OK ] SimdMathTest.copysign (0 ms) 48: [ RUN ] SimdMathTest.invsqrt 48: [ OK ] SimdMathTest.invsqrt (0 ms) 48: [ RUN ] SimdMathTest.maskzInvsqrt 48: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPair 48: [ OK ] SimdMathTest.invsqrtPair (0 ms) 48: [ RUN ] SimdMathTest.sqrt 48: [ OK ] SimdMathTest.sqrt (0 ms) 48: [ RUN ] SimdMathTest.sqrtUnsafe 48: [ OK ] SimdMathTest.sqrtUnsafe (0 ms) 48: [ RUN ] SimdMathTest.inv 48: [ OK ] SimdMathTest.inv (0 ms) 48: [ RUN ] SimdMathTest.maskzInv 48: [ OK ] SimdMathTest.maskzInv (0 ms) 48: [ RUN ] SimdMathTest.cbrt 48: [ OK ] SimdMathTest.cbrt (0 ms) 48: [ RUN ] SimdMathTest.invcbrt 48: [ OK ] SimdMathTest.invcbrt (0 ms) 48: [ RUN ] SimdMathTest.log2 48: [ OK ] SimdMathTest.log2 (0 ms) 48: [ RUN ] SimdMathTest.log 48: [ OK ] SimdMathTest.log (0 ms) 48: [ RUN ] SimdMathTest.exp2 48: [ OK ] SimdMathTest.exp2 (16 ms) 48: [ RUN ] SimdMathTest.exp2Unsafe 48: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 48: [ RUN ] SimdMathTest.exp 48: [ OK ] SimdMathTest.exp (0 ms) 48: [ RUN ] SimdMathTest.expUnsafe 48: [ OK ] SimdMathTest.expUnsafe (0 ms) 48: [ RUN ] SimdMathTest.pow 48: [ OK ] SimdMathTest.pow (0 ms) 48: [ RUN ] SimdMathTest.powUnsafe 48: [ OK ] SimdMathTest.powUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erf 48: [ OK ] SimdMathTest.erf (0 ms) 48: [ RUN ] SimdMathTest.erfc 48: [ OK ] SimdMathTest.erfc (0 ms) 48: [ RUN ] SimdMathTest.sin 48: [ OK ] SimdMathTest.sin (0 ms) 48: [ RUN ] SimdMathTest.cos 48: [ OK ] SimdMathTest.cos (0 ms) 48: [ RUN ] SimdMathTest.tan 48: [ OK ] SimdMathTest.tan (0 ms) 48: [ RUN ] SimdMathTest.asin 48: [ OK ] SimdMathTest.asin (0 ms) 48: [ RUN ] SimdMathTest.acos 48: [ OK ] SimdMathTest.acos (0 ms) 48: [ RUN ] SimdMathTest.atan 48: [ OK ] SimdMathTest.atan (0 ms) 48: [ RUN ] SimdMathTest.atan2 48: [ OK ] SimdMathTest.atan2 (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrection 48: [ OK ] SimdMathTest.pmeForceCorrection (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrection 48: [ OK ] SimdMathTest.pmePotentialCorrection (4 ms) 48: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 48: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracy 48: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.invSingleAccuracy 48: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.cbrtSingleAccuracy 48: [ OK ] SimdMathTest.cbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.invcbrtSingleAccuracy 48: [ OK ] SimdMathTest.invcbrtSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.log2SingleAccuracy 48: [ OK ] SimdMathTest.log2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.logSingleAccuracy 48: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracy 48: [ OK ] SimdMathTest.exp2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 48: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracy 48: [ OK ] SimdMathTest.expSingleAccuracy (8 ms) 48: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracy 48: [ OK ] SimdMathTest.powSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.powSingleAccuracyUnsafe 48: [ OK ] SimdMathTest.powSingleAccuracyUnsafe (0 ms) 48: [ RUN ] SimdMathTest.erfSingleAccuracy 48: [ OK ] SimdMathTest.erfSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.erfcSingleAccuracy 48: [ OK ] SimdMathTest.erfcSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.sinSingleAccuracy 48: [ OK ] SimdMathTest.sinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.cosSingleAccuracy 48: [ OK ] SimdMathTest.cosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.tanSingleAccuracy 48: [ OK ] SimdMathTest.tanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.asinSingleAccuracy 48: [ OK ] SimdMathTest.asinSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.acosSingleAccuracy 48: [ OK ] SimdMathTest.acosSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atanSingleAccuracy 48: [ OK ] SimdMathTest.atanSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.atan2SingleAccuracy 48: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 48: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 48: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 48: [----------] 56 tests from SimdMathTest (43 ms total) 48: 48: [----------] 1 test from EmptyArrayRefTest 48: [ RUN ] EmptyArrayRefTest.IsEmpty 48: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 48: [----------] 1 test from EmptyArrayRefTest (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 48: 48: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 48: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 48: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 48: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 48: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/0.Assignment 48: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefReadWriteTest/1.Assignment 48: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 48: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/0.Basic 48: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 48: 48: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 48: [ RUN ] ArrayRefArithmeticTest/1.Basic 48: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 48: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 48: 48: [----------] 3 tests from SimdVectorOperationsTest 48: [ RUN ] SimdVectorOperationsTest.iprod 48: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 48: [ RUN ] SimdVectorOperationsTest.norm2 48: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 48: [ RUN ] SimdVectorOperationsTest.cprod 48: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 48: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 48: 48: [----------] 32 tests from Simd4FloatingpointTest 48: [ RUN ] Simd4FloatingpointTest.setZero 48: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 48: [ RUN ] Simd4FloatingpointTest.set 48: [ OK ] Simd4FloatingpointTest.set (0 ms) 48: [ RUN ] Simd4FloatingpointTest.add 48: [ OK ] Simd4FloatingpointTest.add (0 ms) 48: [ RUN ] Simd4FloatingpointTest.sub 48: [ OK ] Simd4FloatingpointTest.sub (0 ms) 48: [ RUN ] Simd4FloatingpointTest.mul 48: [ OK ] Simd4FloatingpointTest.mul (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fma 48: [ OK ] Simd4FloatingpointTest.fma (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fms 48: [ OK ] Simd4FloatingpointTest.fms (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fnma 48: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 48: [ RUN ] Simd4FloatingpointTest.fnms 48: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 48: [ RUN ] Simd4FloatingpointTest.abs 48: [ OK ] Simd4FloatingpointTest.abs (0 ms) 48: [ RUN ] Simd4FloatingpointTest.neg 48: [ OK ] Simd4FloatingpointTest.neg (0 ms) 48: [ RUN ] Simd4FloatingpointTest.and 48: [ OK ] Simd4FloatingpointTest.and (0 ms) 48: [ RUN ] Simd4FloatingpointTest.or 48: [ OK ] Simd4FloatingpointTest.or (0 ms) 48: [ RUN ] Simd4FloatingpointTest.xor 48: [ OK ] Simd4FloatingpointTest.xor (0 ms) 48: [ RUN ] Simd4FloatingpointTest.andNot 48: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 48: [ RUN ] Simd4FloatingpointTest.max 48: [ OK ] Simd4FloatingpointTest.max (0 ms) 48: [ RUN ] Simd4FloatingpointTest.min 48: [ OK ] Simd4FloatingpointTest.min (0 ms) 48: [ RUN ] Simd4FloatingpointTest.round 48: [ OK ] Simd4FloatingpointTest.round (0 ms) 48: [ RUN ] Simd4FloatingpointTest.trunc 48: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 48: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 48: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 48: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 48: [ RUN ] Simd4FloatingpointTest.selectByNotMask 48: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpNe 48: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpLe 48: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 48: [ RUN ] Simd4FloatingpointTest.cmpLt 48: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 48: [ RUN ] Simd4FloatingpointTest.andB 48: [ OK ] Simd4FloatingpointTest.andB (0 ms) 48: [ RUN ] Simd4FloatingpointTest.orB 48: [ OK ] Simd4FloatingpointTest.orB (0 ms) 48: [ RUN ] Simd4FloatingpointTest.anyTrue 48: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 48: [ RUN ] Simd4FloatingpointTest.blend 48: [ OK ] Simd4FloatingpointTest.blend (0 ms) 48: [ RUN ] Simd4FloatingpointTest.reduce 48: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 48: [ RUN ] Simd4FloatingpointTest.dotProduct 48: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 48: [ RUN ] Simd4FloatingpointTest.transpose 48: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 48: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 48: 48: [----------] 2 tests from Simd4MathTest 48: [ RUN ] Simd4MathTest.invsqrt 48: [ OK ] Simd4MathTest.invsqrt (0 ms) 48: [ RUN ] Simd4MathTest.invsqrtSingleAccuracy 48: [ OK ] Simd4MathTest.invsqrtSingleAccuracy (0 ms) 48: [----------] 2 tests from Simd4MathTest (0 ms total) 48: 48: [----------] 1 test from Simd4VectorOperationsTest 48: [ RUN ] Simd4VectorOperationsTest.norm2 48: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 48: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 48: 48: [----------] Global test environment tear-down 48: [==========] 288 tests from 22 test suites ran. (44 ms total) 48: [ PASSED ] 288 tests. 48/91 Test #48: SimdUnitTests ................................ Passed 0.20 sec test 49 Start 49: CompatibilityHelpersTests 49: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/compat-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/CompatibilityHelpersTests.xml" 49: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/compat/tests 49: Test timeout computed to be: 30 49: [==========] Running 9 tests from 6 test suites. 49: [----------] Global test environment set-up. 49: [----------] 4 tests from TemplateMPTest 49: [ RUN ] TemplateMPTest.MpWithIndexInt 49: [ OK ] TemplateMPTest.MpWithIndexInt (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexIntBad 49: [ OK ] TemplateMPTest.MpWithIndexIntBad (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexBool 49: [ OK ] TemplateMPTest.MpWithIndexBool (0 ms) 49: [ RUN ] TemplateMPTest.MpWithIndexEnum 49: [ OK ] TemplateMPTest.MpWithIndexEnum (0 ms) 49: [----------] 4 tests from TemplateMPTest (0 ms total) 49: 49: [----------] 1 test from NotNullConstruction 49: [ RUN ] NotNullConstruction.Works 49: [ OK ] NotNullConstruction.Works (0 ms) 49: [----------] 1 test from NotNullConstruction (0 ms total) 49: 49: [----------] 1 test from NotNullCasting 49: [ RUN ] NotNullCasting.Works 49: [ OK ] NotNullCasting.Works (0 ms) 49: [----------] 1 test from NotNullCasting (0 ms total) 49: 49: [----------] 1 test from NotNullAssignment 49: [ RUN ] NotNullAssignment.Works 49: [ OK ] NotNullAssignment.Works (0 ms) 49: [----------] 1 test from NotNullAssignment (0 ms total) 49: 49: [----------] 1 test from MakeNotNull 49: [ RUN ] MakeNotNull.Works 49: [ OK ] MakeNotNull.Works (0 ms) 49: [----------] 1 test from MakeNotNull (0 ms total) 49: 49: [----------] 1 test from NotNull 49: [ RUN ] NotNull.WorksInContainers 49: [ OK ] NotNull.WorksInContainers (0 ms) 49: [----------] 1 test from NotNull (0 ms total) 49: 49: [----------] Global test environment tear-down 49: [==========] 9 tests from 6 test suites ran. (0 ms total) 49: [ PASSED ] 9 tests. 49/91 Test #49: CompatibilityHelpersTests .................... Passed 0.30 sec test 50 Start 50: GmxAnaTest 50: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxana-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxAnaTest.xml" 50: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxana/tests 50: Test timeout computed to be: 600 50: [==========] Running 31 tests from 4 test suites. 50: [----------] Global test environment set-up. 50: [----------] 7 tests from Entropy 50: [ RUN ] Entropy.Schlitter_300_NoLinear 50: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 50: [ RUN ] Entropy.Schlitter_300_Linear 50: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 50: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 50: [ RUN ] Entropy.QuasiHarmonic_200_Linear 50: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_200_Linear 50: [ OK ] Entropy.EntropyCompare_200_Linear (0 ms) 50: [ RUN ] Entropy.EntropyCompare_300_Linear 50: [ OK ] Entropy.EntropyCompare_300_Linear (0 ms) 50: [----------] 7 tests from Entropy (0 ms total) 50: 50: [----------] 2 tests from GmxChiTest 50: [ RUN ] GmxChiTest.gmxchiWorksWithAll 50: Analyzing from residue 1 to residue 11 50: 10 residues with dihedrals found 50: 46 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 46 50: Printing phiLYS1.xvg Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing phiGLU7.xvg Printing phiLEU8.xvg Printing phiALA9.xvg Printing phiALA10.xvg Printing psiLYS1.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing psiGLU7.xvg Printing psiLEU8.xvg Printing psiALA9.xvg Printing psiALA10.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing omegaGLU7.xvg Printing omegaLEU8.xvg Printing omegaALA9.xvg Printing omegaALA10.xvg Printing chi1LYS1.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi1GLU7.xvg Printing chi1LEU8.xvg Printing chi2LYS1.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi2GLU7.xvg Printing chi2LEU8.xvg Printing chi3LYS1.xvg Printing chi3ARG5.xvg Printing chi3GLU7.xvg Printing chi4LYS1.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductLYS1.xvg and histo-chiprodLYS1.xvg Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg Printing chiproductGLU7.xvg and histo-chiprodGLU7.xvg Printing chiproductLEU8.xvg and histo-chiprodLEU8.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithAll (1740 ms) 50: [ RUN ] GmxChiTest.gmxchiWorksWithr0AndrN 50: Analyzing from residue 2 to residue 6 50: 5 residues with dihedrals found 50: 23 dihedrals found 50: Reading frames from gro file 'First 10 residues from 1AKI t= 0.00000 step= 0', 156 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 0.020 Reading frame 2 time 0.040 Last frame 2 time 0.040 50: j after resetting (nr. active dihedrals) = 23 50: Printing phiVAL2.xvg Printing phiPHE3.xvg Printing phiGLY4.xvg Printing phiARG5.xvg Printing phiCYS6.xvg Printing psiVAL2.xvg Printing psiPHE3.xvg Printing psiGLY4.xvg Printing psiARG5.xvg Printing psiCYS6.xvg Printing omegaVAL2.xvg Printing omegaPHE3.xvg Printing omegaGLY4.xvg Printing omegaARG5.xvg Printing omegaCYS6.xvg Printing chi1VAL2.xvg Printing chi1PHE3.xvg Printing chi1ARG5.xvg Printing chi1CYS6.xvg Printing chi2PHE3.xvg Printing chi2ARG5.xvg Printing chi3ARG5.xvg Printing chi4ARG5.xvg 50: Now calculating transitions... 50: Total number of transitions: 0 50: Now printing out transitions and OPs... 50: Now printing out rotamer occupancies... 50: Now calculating Chi product trajectories... 50: Printing chiproductVAL2.xvg and histo-chiprodVAL2.xvg Printing chiproductPHE3.xvg and histo-chiprodPHE3.xvg Printing chiproductARG5.xvg and histo-chiprodARG5.xvg Printing chiproductCYS6.xvg and histo-chiprodCYS6.xvg 50: [ OK ] GmxChiTest.gmxchiWorksWithr0AndrN (720 ms) 50: [----------] 2 tests from GmxChiTest (2654 ms total) 50: 50: [----------] 10 tests from MindistTest 50: [ RUN ] MindistTest.mindistWorksWithSingleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistWorksWithSingleAtoms (10 ms) 50: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (0 ms) 50: [ RUN ] MindistTest.mindistDoesNotPickUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistDoesNotPickUpContacts (0 ms) 50: [ RUN ] MindistTest.mindistPicksUpContacts 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.mindistPicksUpContacts (0 ms) 50: [ RUN ] MindistTest.ngWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.ngWorks (0 ms) 50: [ RUN ] MindistTest.groupWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.groupWorks (0 ms) 50: [ RUN ] MindistTest.maxDistWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 2: 'atom3' 50: Selected 3: 'atoms12' 50: [ OK ] MindistTest.maxDistWorks (0 ms) 50: [ RUN ] MindistTest.noPbcWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 0: 'atom1' 50: Selected 1: 'atom2' 50: [ OK ] MindistTest.noPbcWorks (0 ms) 50: [ RUN ] MindistTest.resPerTimeWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 3: 'atoms12' 50: Selected 2: 'atom3' 50: [ OK ] MindistTest.resPerTimeWorks (8 ms) 50: [ RUN ] MindistTest.matrixWorks 50: Group 0 ( atom1) has 1 elements 50: Group 1 ( atom2) has 1 elements 50: Group 2 ( atom3) has 1 elements 50: Group 3 ( atoms12) has 2 elements 50: Group 4 ( atoms23) has 2 elements 50: Group 5 ( atoms123) has 3 elements 50: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms. 50: Reading frame 0 time 0.000 Last frame 0 time 0.000 50: Selected 5: 'atoms123' 50: Special case: making distance matrix between all atoms in group atoms123 50: [ OK ] MindistTest.matrixWorks (0 ms) 50: [----------] 10 tests from MindistTest (22 ms total) 50: 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: trr version: GMX_trn_file (single precision) 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (0 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (5 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/0 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/1 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 50: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/2 (5 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/3 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/4 (1 ms) 50: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 50: Group 0 ( System) has 6 elements 50: Group 1 ( Water) has 6 elements 50: Group 2 ( SOL) has 6 elements 50: Select a group: Reading frame 0 time 0.000 50: WARNING: If there are molecules in the input trajectory file 50: that are broken across periodic boundaries, they 50: cannot be made whole (or treated as whole) without 50: you providing a run input file. 50: 50: Reading frame 1 time 1.000 Last frame 1 time 1.000 50: 50: WARNING: Masses and atomic (Van der Waals) radii will be guessed 50: based on residue and atom names, since they could not be 50: definitively assigned from the information in your input 50: files. These guessed numbers might deviate from the mass 50: and radius of the atom type. Please check the output 50: files if necessary. Note, that this functionality may 50: be removed in a future GROMACS version. Please, consider 50: using another file format for your input. 50: 50: Selected 0: 'System' 50: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.RotationalKineticEnergy/5 (5 ms) 50: [----------] 12 tests from NoFatalErrorWhenWritingFrom/GmxTraj (23 ms total) 50: 50: [----------] Global test environment tear-down 50: [==========] 31 tests from 4 test suites ran. (2701 ms total) 50: [ PASSED ] 31 tests. 50/91 Test #50: GmxAnaTest ................................... Passed 2.90 sec test 51 Start 51: GmxPreprocessTests 51: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxpreprocess-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/GmxPreprocessTests.xml" 51: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 51: Test timeout computed to be: 1920 51: [==========] Running 138 tests from 13 test suites. 51: [----------] Global test environment set-up. 51: [----------] 4 tests from GenconfTest 51: [ RUN ] GenconfTest.nbox_Works 51: [ OK ] GenconfTest.nbox_Works (1 ms) 51: [ RUN ] GenconfTest.nbox_norenumber_Works 51: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_dist_Works 51: [ OK ] GenconfTest.nbox_dist_Works (0 ms) 51: [ RUN ] GenconfTest.nbox_rot_Works 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: center of geometry: 1.733667, 1.477000, 0.905167 51: [ OK ] GenconfTest.nbox_rot_Works (0 ms) 51: [----------] 4 tests from GenconfTest (2 ms total) 51: 51: [----------] 2 tests from GenionTest 51: [ RUN ] GenionTest.HighConcentrationIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: Group 0 ( System) has 653 elements 51: Group 1 ( Water) has 648 elements 51: Group 2 ( SOL) has 648 elements 51: Group 3 ( non-Water) has 5 elements 51: Group 4 ( Other) has 5 elements 51: Group 5 ( METH) has 5 elements 51: Select a group: Number of (3-atomic) solvent molecules: 216 51: Using random seed 1997. 51: Replacing solvent molecule 56 (atom 168) with NA 51: Replacing solvent molecule 120 (atom 360) with NA 51: Replacing solvent molecule 182 (atom 546) with NA 51: Replacing solvent molecule 71 (atom 213) with NA 51: Replacing solvent molecule 189 (atom 567) with CL 51: Replacing solvent molecule 54 (atom 162) with CL 51: Replacing solvent molecule 155 (atom 465) with CL 51: Replacing solvent molecule 99 (atom 297) with CL 51: 51: Setting the LD random seed to -1751454721 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: Will try to add 4 NA ions and 4 CL ions. 51: Select a continuous group of solvent molecules 51: Selected 1: 'Water' 51: [ OK ] GenionTest.HighConcentrationIonPlacement (581 ms) 51: [ RUN ] GenionTest.NoIonPlacement 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet 51: buffer. The cluster pair list does have a buffering effect, but choosing 51: a larger rlist might be necessary for good energy conservation. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 51: < 0 51: 51: 51: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: Generating 1-4 interactions: fudge = 0.5 51: Number of degrees of freedom in T-Coupling group rest is 1308.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]: 51: You are using a plain Coulomb cut-off, which might produce artifacts. 51: You might want to consider using PME electrostatics. 51: 51: 51: 51: There were 4 NOTEs 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: No ions to add, will just copy input configuration. 51: Setting the LD random seed to -35659814 51: 51: Generated 331705 of the 331705 non-bonded parameter combinations 51: 51: Generated 331705 of the 331705 1-4 parameter combinations 51: 51: Excluding 2 bonded neighbours molecule type 'SOL' 51: 51: Excluding 3 bonded neighbours molecule type 'methane' 51: Analysing residue names: 51: There are: 216 Water residues 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GenionTest.NoIonPlacement (421 ms) 51: [----------] 2 tests from GenionTest (1002 ms total) 51: 51: [----------] 1 test from GenRestrTest 51: [ RUN ] GenRestrTest.SimpleRestraintsGenerated 51: 51: Reading structure file 51: Group 0 ( System) has 156 elements 51: Group 1 ( Protein) has 156 elements 51: Group 2 ( Protein-H) has 75 elements 51: Group 3 ( C-alpha) has 10 elements 51: Group 4 ( Backbone) has 30 elements 51: Group 5 ( MainChain) has 40 elements 51: Group 6 ( MainChain+Cb) has 49 elements 51: Group 7 ( MainChain+H) has 52 elements 51: Group 8 ( SideChain) has 104 elements 51: Group 9 ( SideChain-H) has 35 elements 51: Select a group: Select group to position restrain 51: Selected 3: 'C-alpha' 51: [ OK ] GenRestrTest.SimpleRestraintsGenerated (0 ms) 51: [----------] 1 test from GenRestrTest (1 ms total) 51: 51: [----------] 9 tests from PreprocessingAtomTypesTest 51: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate 51: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks 51: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound 51: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total) 51: 51: [----------] 10 tests from PreprocessingBondAtomTypeTest 51: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate 51: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid 51: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks 51: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry 51: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType 51: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound 51: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms) 51: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber 51: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms) 51: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total) 51: 51: [----------] 1 test from GromppDirectiveTest 51: [ RUN ] GromppDirectiveTest.edgeCaseAtomTypeNames 51: Ignoring obsolete mdp entry 'title' 51: Generating 1-4 interactions: fudge = 0.5 51: 51: NOTE 1 [file directives.top, line 44]: 51: In moleculetype 'A' 2 atoms are not bound by a potential or constraint to 51: any other atom in the same moleculetype. Although technically this might 51: not cause issues in a simulation, this often means that the user forgot 51: to add a bond/potential/constraint or put multiple molecules in the same 51: moleculetype definition by mistake. Run with -v to get information for 51: each atom. 51: 51: Number of degrees of freedom in T-Coupling group rest is 9.00 51: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.mdp]: 51: NVE simulation: will use the initial temperature of 300.000 K for 51: determining the Verlet buffer size 51: 51: 51: There were 2 NOTEs 51: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GromppDirectiveTest_edgeCaseAtomTypeNames_directives.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 51: Setting the LD random seed to 348104391 51: 51: Generated 10 of the 10 non-bonded parameter combinations 51: 51: Generated 10 of the 10 1-4 parameter combinations 51: 51: Excluding 0 bonded neighbours molecule type 'A' 51: 51: Setting gen_seed to 2060954516 51: 51: Velocities were taken from a Maxwell distribution at 300 K 51: Analysing residue names: 51: There are: 1 Other residues 51: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 51: 51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 51: 51: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 51: 51: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 51: 51: Note that mdrun will redetermine rlist based on the actual pair-list setup 51: 51: This run will generate roughly 0 Mb of data 51: [ OK ] GromppDirectiveTest.edgeCaseAtomTypeNames (2 ms) 51: [----------] 1 test from GromppDirectiveTest (2 ms total) 51: 51: [----------] 5 tests from InsertMoleculesTest 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: 51: Added 1 molecules (out of 1 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 51: 51: Output configuration contains 8 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (0 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 success (now 6 atoms)! 51: Try 4 success (now 8 atoms)! 51: Try 5 success (now 10 atoms)! 51: 51: Added 5 molecules (out of 5 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 51: 51: Output configuration contains 10 atoms in 10 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (1 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 8 atoms)! 51: Try 2 success (now 10 atoms)! 51: 51: Added 2 molecules (out of 2 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 51: 51: Output configuration contains 10 atoms in 4 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (0 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 51: Reading solute configuration 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Try 1 success (now 650 atoms)! 51: Try 2 success (now 652 atoms)! 51: Try 3 success (now 654 atoms)! 51: Try 4 success (now 656 atoms)! 51: 51: Added 4 molecules (out of 4 requested) 51: Replaced 8 residues (24 atoms) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 51: 51: Output configuration contains 632 atoms in 212 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (11 ms) 51: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Using random seed 1997 51: Read 4 positions from file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 51: 51: Try 1 success (now 2 atoms)! 51: Try 2 success (now 4 atoms)! 51: Try 3 Try 4 Try 5 Try 6 Try 7 Try 8 Try 9 Try 10 Try 11 Try 12 skipped position (0.990, 2.010, 3.000) 51: Try 13 success (now 6 atoms)! 51: 51: Added 3 molecules (out of 4 requested) 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 51: 51: Output configuration contains 6 atoms in 3 residues 51: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (0 ms) 51: [----------] 5 tests from InsertMoleculesTest (14 ms total) 51: 51: [----------] 3 tests from MassRepartitioning 51: [ RUN ] MassRepartitioning.ValidCaseWorks 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.ValidCaseWorks (0 ms) 51: [ RUN ] MassRepartitioning.UnboundGivesWarning 51: 51: WARNING 1 [file unknown]: 51: The are 1 atoms that have a mass below the mass repartitioning limit but 51: are not bound. These masses cannot be repartitioned. 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.UnboundGivesWarning (0 ms) 51: [ RUN ] MassRepartitioning.LightPartnerGivesError 51: 51: ERROR 1 [file unknown]: 51: Light atoms are bound to at least one atom that has a too low mass for 51: repartioning 51: 51: The smallest mass in the system is 2, setting the minimum mass to 6 51: [ OK ] MassRepartitioning.LightPartnerGivesError (0 ms) 51: [----------] 3 tests from MassRepartitioning (0 ms total) 51: 51: [----------] 35 tests from GetIrTest 51: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 51: Ignoring obsolete mdp entry 'title' 51: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (1 ms) 51: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals 51: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (0 ms) 51: [ RUN ] GetIrTest.AcceptsKeyWithoutValue 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsKeyWithoutValue (1 ms) 51: [ RUN ] GetIrTest.RejectsValueWithoutKey 51: [ OK ] GetIrTest.RejectsValueWithoutKey (0 ms) 51: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue 51: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (0 ms) 51: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (1 ms) 51: [ RUN ] GetIrTest.AcceptsEmptyLines 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsEmptyLines (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstcalcenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: With MTS, nstcalcenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstcalcenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstcalcenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstenergy 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: With MTS, nstenergy = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstenergy (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstenergy_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckNstenergy (1 ms) 51: [ RUN ] GetIrTest.MtsCheckNstpcouple 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp, line 7]: 51: Pressure coupling incorrect number of values (I need exactly 1) 51: 51: 51: ERROR 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: With multiple time stepping, nstpcouple should be a multiple of 51: mts-factor 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: The Berendsen barostat does not generate any strictly correct ensemble, 51: and should not be used for new production simulations (in our opinion). 51: We recommend using the C-rescale barostat instead. 51: 51: 51: ERROR 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstpcouple_input.mdp]: 51: compressibility must be > 0 when using pressure coupling Berendsen 51: 51: 51: [ OK ] GetIrTest.MtsCheckNstpcouple (9 ms) 51: [ RUN ] GetIrTest.MtsCheckNstdhdl 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: With MTS, nstdhdl = 5 should be a multiple of mts-factor = 2 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Setting nstcalcenergy (100) equal to nstdhdl (5) 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: 51: ERROR 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckNstdhdl_input.mdp]: 51: Lambda state must be set, either with init-lambda-state or with 51: init-lambda 51: 51: [ OK ] GetIrTest.MtsCheckNstdhdl (1 ms) 51: [ RUN ] GetIrTest.MtsCheckSDNotSupported 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: Multiple time stepping is only supported with integrator md 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MtsCheckSDNotSupported_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MtsCheckSDNotSupported (1 ms) 51: [ RUN ] GetIrTest.AcceptsElectricField 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricField (1 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (1 ms) 51: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (1 ms) 51: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys 51: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (0 ms) 51: [ RUN ] GetIrTest.AcceptsImplicitSolventNo 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsImplicitSolventNo (1 ms) 51: [ RUN ] GetIrTest.RejectsImplicitSolventYes 51: [ OK ] GetIrTest.RejectsImplicitSolventYes (0 ms) 51: [ RUN ] GetIrTest.AcceptsMimic 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsMimic (1 ms) 51: [ RUN ] GetIrTest.AcceptsTransformationCoord 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp, line 11]: 51: pull-coord2 has a non-zero force constant and is also referenced in 51: pull-coord1-expression. Make sure that this is intended. In most use 51: cases, the pull coordinates referenced by a transformation coordinate 51: should have their force constant set to zero. 51: 51: 51: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsTransformationCoord_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.AcceptsTransformationCoord (10 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordWithConstraint 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp, line 7]: 51: pull-coord1 cannot have type 'constraint' and geometry 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordWithConstraint_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordWithConstraint (1 ms) 51: [ RUN ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp, line 10]: 51: pull-coord2 can not use pull-coord1 in the transformation since this is a 51: constraint 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidPullCoordWithConstraintInTransformationExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidPullCoordWithConstraintInTransformationExpression (1 ms) 51: [ RUN ] GetIrTest.InvalidTransformationCoordDxValue 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp, line 7]: 51: pull-coord1-dx cannot be set to zero for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_InvalidTransformationCoordDxValue_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.InvalidTransformationCoordDxValue (1 ms) 51: [ RUN ] GetIrTest.MissingTransformationCoordExpression 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp, line 5]: 51: pull-coord1-expression not set for pull coordinate of geometry 51: 'transformation' 51: 51: 51: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_MissingTransformationCoordExpression_input.mdp]: 51: For a correct single-point energy evaluation with nsteps = 0, use 51: continuation = yes to avoid constraining the input coordinates. 51: 51: [ OK ] GetIrTest.MissingTransformationCoordExpression (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_input.mdp]: 51: With init-lambda = 0 and delta_lambda = 1e-05 and no explicit input, 51: coul-lambdas and vdw-lambdas will be greater than 1 after step 100000 of 51: in total 100001 steps. This is not compatible with using soft-core 51: potentials. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_SC_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda = 1 and delta_lambda = -1e-05, the lambda components 51: won't change anymore after step 100000 until the end of the simulation 51: after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_NoSC_And_OneStepTooMuch_negativeDelta (9 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_input.mdp]: 51: With init-lambda-state = 0 and delta_lambda = 1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta 51: 51: ERROR 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta_input.mdp]: 51: With init-lambda-state = 2 and delta_lambda = -1e-05, the lambda 51: components won't change anymore after step 100000 until the end of the 51: simulation after 100001 steps. 51: 51: 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_OneStepTooMuch_negativeDelta (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep (1 ms) 51: [ RUN ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta 51: [ OK ] GetIrTest.lambdaOverOneCheck_LambdaVector_And_ExactlyAsManyStep_negativeDelta (1 ms) 51: [----------] 35 tests from GetIrTest (67 ms total) 51: 51: [----------] 6 tests from SolvateTest 51: [ RUN ] SolvateTest.cs_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 1x1x1 boxes 51: Solvent box contains 270 atoms in 90 residues 51: Removed 129 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 47 residues 51: Generated solvent containing 141 atoms in 47 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 51: 51: Output configuration contains 141 atoms in 47 residues 51: Volume : 1.331 (nm^3) 51: Density : 1056.36 (g/l) 51: Number of solvent molecules: 47 51: 51: [ OK ] SolvateTest.cs_box_Works (2 ms) 51: [ RUN ] SolvateTest.cs_cp_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: [ OK ] SolvateTest.cs_cp_Works (27 ms) 51: [ RUN ] SolvateTest.cs_cp_p_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 886 residues 51: Generated solvent containing 2658 atoms in 886 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 51: 51: Output configuration contains 2664 atoms in 888 residues 51: Volume : 27.2709 (nm^3) 51: Density : 974.777 (g/l) 51: Number of solvent molecules: 886 51: 51: Processing topology 51: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top) 51: [ OK ] SolvateTest.cs_cp_p_Works (16 ms) 51: [ RUN ] SolvateTest.shell_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 3660 atoms in 1220 residues 51: Removed 987 solvent atoms due to solvent-solvent overlap 51: Removed 1902 solvent atoms more than 1.000000 nm from solute. 51: Removed 15 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 252 residues 51: Generated solvent containing 756 atoms in 252 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 51: 51: Output configuration contains 762 atoms in 254 residues 51: Volume : 27.2709 (nm^3) 51: Density : 279.3 (g/l) 51: Number of solvent molecules: 252 51: 51: [ OK ] SolvateTest.shell_Works (15 ms) 51: [ RUN ] SolvateTest.update_Topology_Works 51: Reading solute configuration 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 3x3x3 boxes 51: Solvent box contains 14952 atoms in 4984 residues 51: Removed 2787 solvent atoms due to solvent-solvent overlap 51: Removed 30 solvent atoms due to solute-solvent overlap 51: Sorting configuration 51: Found 2 different molecule types: 51: HOH ( 3 atoms): 1876 residues 51: SOL ( 3 atoms): 2169 residues 51: Generated solvent containing 0 atoms in 0 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 51: 51: Output configuration contains 12141 atoms in 4047 residues 51: Volume : 125 (nm^3) 51: Density : 968.963 (g/l) 51: Number of solvent molecules: 4045 51: 51: Processing topology 51: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 51: [ OK ] SolvateTest.update_Topology_Works (114 ms) 51: [ RUN ] SolvateTest.cs_pdb_big_box_Works 51: Reading solvent configuration 51: 51: Initialising inter-atomic distances... 51: 51: WARNING: Masses and atomic (Van der Waals) radii will be guessed 51: based on residue and atom names, since they could not be 51: definitively assigned from the information in your input 51: files. These guessed numbers might deviate from the mass 51: and radius of the atom type. Please check the output 51: files if necessary. Note, that this functionality may 51: be removed in a future GROMACS version. Please, consider 51: using another file format for your input. 51: 51: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 51: from the source below. This means the results may be different 51: compared to previous GROMACS versions. 51: 51: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 51: A. Bondi 51: van der Waals Volumes and Radii 51: J. Phys. Chem. 68 (1964) pp. 441-451 51: -------- -------- --- Thank You --- -------- -------- 51: 51: Generating solvent configuration 51: Will generate new solvent configuration of 2x2x2 boxes 51: Solvent box contains 1218 atoms in 406 residues 51: Removed 555 solvent atoms due to solvent-solvent overlap 51: Sorting configuration 51: Found 1 molecule type: 51: SOL ( 3 atoms): 221 residues 51: Generated solvent containing 663 atoms in 221 residues 51: Writing generated configuration to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_pdb_big_box_Works_out.gro 51: 51: Output configuration contains 663 atoms in 221 residues 51: Volume : 8 (nm^3) 51: Density : 826.409 (g/l) 51: Number of solvent molecules: 221 51: 51: [ OK ] SolvateTest.cs_pdb_big_box_Works (4 ms) 51: [----------] 6 tests from SolvateTest (181 ms total) 51: 51: [----------] 1 test from TopDirTests 51: [ RUN ] TopDirTests.NamesArrayHasCorrectSize 51: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms) 51: [----------] 1 test from TopDirTests (0 ms total) 51: 51: [----------] 45 tests from SinglePeptideFragments/EditconfTest 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (16 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (6 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (12 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (11 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (10 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (12 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (0 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 51: 51: Select a group for output: 51: Group 0 ( two_residues) has 23 elements 51: There is one group in the index 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (13 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/0 (5 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/1 (18 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/2 (13 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/3 (15 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/5 (14 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/6 (12 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : 0.212 1.187 3.527 (nm) 51: new center : 4.028 2.819 3.723 (nm) 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenter/8 (6 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/0 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/1 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.42 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/2 (12 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/3 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/5 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/6 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/7 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: shift : -0.814 1.104 2.657 (nm) 51: new center : 3.002 2.736 2.852 (nm) 51: new box vectors : 6.004 5.472 5.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 187.40 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesCenterAndDiameter/8 (12 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/0 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/1 (6 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.28 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/2 (14 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/3 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/4 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/5 (2 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/6 (1 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/7 (13 ms) 51: [ RUN ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 51: Note that major changes are planned in future for editconf, to improve usability and utility. 51: Read 252 atoms 51: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons 51: No velocities found 51: system size : 2.004 1.472 1.704 (nm) 51: center : 3.816 1.632 0.195 (nm) 51: box vectors : 8.056 5.637 7.445 (nm) 51: box angles : 90.00 90.00 90.00 (degrees) 51: box volume : 338.10 (nm^3) 51: new center : 3.816 1.632 0.195 (nm) 51: new box vectors : 5.004 4.472 4.704 (nm) 51: new box angles : 90.00 90.00 90.00 (degrees) 51: new box volume : 105.27 (nm^3) 51: 51: WARNING: No boxtype specified - distance condition applied in each dimension. 51: If the molecule rotates the actual distance will be smaller. You might want 51: to use a cubic box instead, or why not try a dodecahedron today? 51: [ OK ] SinglePeptideFragments/EditconfTest.HandlesBothNoCenterAndDiameter/8 (1 ms) 51: [----------] 45 tests from SinglePeptideFragments/EditconfTest (271 ms total) 51: 51: [----------] 16 tests from CorrectVelocity/MaxwellTest 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/0 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/0 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/1 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/1 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/2 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/2 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/3 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/3 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/4 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/4 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/5 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/5 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/6 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/6 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/7 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/7 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/8 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/8 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/9 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/9 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/10 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/10 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/11 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/11 (12 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/12 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/12 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/13 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/13 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/14 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/14 (0 ms) 51: [ RUN ] CorrectVelocity/MaxwellTest.CreationWorks/15 51: [ OK ] CorrectVelocity/MaxwellTest.CreationWorks/15 (0 ms) 51: [----------] 16 tests from CorrectVelocity/MaxwellTest (20 ms total) 51: 51: [----------] Global test environment tear-down 51: [==========] 138 tests from 13 test suites ran. (1564 ms total) 51: [ PASSED ] 138 tests. 51/91 Test #51: GmxPreprocessTests ........................... Passed 1.77 sec test 52 Start 52: Pdb2gmx1Test 52: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pdb2gmx1-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Pdb2gmx1Test.xml" 52: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 52: Test timeout computed to be: 1920 52: [==========] Running 30 tests from 1 test suite. 52: [----------] Global test environment set-up. 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (35 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (39 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (34 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (37 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (98 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (62 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (80 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (62 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (77 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip3p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (220 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (77 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (74 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (41 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (32 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (171 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (63 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (60 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (53 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (58 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip4p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip4p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (180 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 0 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (53 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 0 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (79 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 0 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (69 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 0 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (72 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 0 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (102 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 25 donors and 23 acceptors were found. 52: There are 41 hydrogen bonds 52: Will use HISE for residue 8 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS3 HIS8 52: SG9 NE251 52: HIS8 NE251 1.055 52: MET12 SD83 0.763 0.990 52: Marked 124 virtual sites 52: Added 16 dummy masses 52: Added 26 new constraints 52: Before cleaning: 653 pairs 52: Before cleaning: 663 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 52: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 128 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (128 atoms, 16 residues) 52: 52: Identified residue ALA2 as a starting terminus. 52: 52: Identified residue SER17 as a ending terminus. 52: Start terminus ALA-2: NH3+ 52: End terminus SER-17: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 252 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 254, now 254 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 663 dihedrals, 51 impropers, 457 angles 52: 650 pairs, 254 bonds and 130 virtual sites 52: 52: Total mass 1846.112 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (35 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 30 donors and 22 acceptors were found. 52: There are 36 hydrogen bonds 52: Will use HISE for residue 29 52: Will use HISE for residue 32 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS27 HIS29 52: SG90 NE2111 52: HIS29 NE2111 0.987 52: HIS32 NE2135 1.590 1.155 52: Marked 132 virtual sites 52: Added 10 dummy masses 52: Added 19 new constraints 52: Before cleaning: 748 pairs 52: Before cleaning: 778 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 52: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 149 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (149 atoms, 16 residues) 52: 52: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue THR18 as a starting terminus. 52: 52: Identified residue PHE33 as a ending terminus. 52: Start terminus THR-18: NH3+ 52: End terminus PHE-33: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 281 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 290, now 290 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 778 dihedrals, 72 impropers, 516 angles 52: 736 pairs, 290 bonds and 133 virtual sites 52: 52: Total mass 2088.357 a.m.u. 52: 52: Total charge 1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (44 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 22 acceptors were found. 52: There are 26 hydrogen bonds 52: Will use HISE for residue 45 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS45 52: NE295 52: MET46 SD102 1.078 52: Marked 123 virtual sites 52: Added 22 dummy masses 52: Added 35 new constraints 52: Before cleaning: 676 pairs 52: Before cleaning: 696 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 52: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 132 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (132 atoms, 16 residues) 52: 52: Identified residue ALA34 as a starting terminus. 52: 52: Identified residue ALA49 as a ending terminus. 52: Start terminus ALA-34: NH3+ 52: End terminus ALA-49: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 255 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 261, now 261 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 696 dihedrals, 56 impropers, 472 angles 52: 667 pairs, 261 bonds and 132 virtual sites 52: 52: Total mass 1861.128 a.m.u. 52: 52: Total charge -1.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (39 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 22 donors and 21 acceptors were found. 52: There are 30 hydrogen bonds 52: Will use HISE for residue 60 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: HIS60 52: NE285 52: CYS62 SG98 0.803 52: Marked 111 virtual sites 52: Added 18 dummy masses 52: Added 31 new constraints 52: Before cleaning: 603 pairs 52: Before cleaning: 618 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 52: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 52: 52: chain #res #atoms 52: 52: 1 ' ' 16 117 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 (117 atoms, 16 residues) 52: 52: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 52: 52: Identified residue LYS50 as a starting terminus. 52: 52: Identified residue PRO65 as a ending terminus. 52: Start terminus LYS-50: NH3+ 52: End terminus PRO-65: PRO-COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 16 residues with 228 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 232, now 232 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 618 dihedrals, 48 impropers, 419 angles 52: 597 pairs, 232 bonds and 116 virtual sites 52: 52: Total mass 1662.883 a.m.u. 52: 52: Total charge -0.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (30 ms) 52: [ RUN ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.r2b 52: All occupancies are one 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/atomtypes.atp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.rtp 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.hdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.n.tdb 52: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/oplsaa.ff/aminoacids.c.tdb 52: Analysing hydrogen-bonding network for automated assignment of histidine 52: protonation. 89 donors and 98 acceptors were found. 52: There are 129 hydrogen bonds 52: Will use HISE for residue 31 52: Will use HISE for residue 51 52: 9 out of 9 lines of specbond.dat converted successfully 52: Special Atom Distance matrix: 52: CYS25 HIS31 HIS51 52: SG14 NE264 NE2226 52: HIS31 NE264 1.921 52: HIS51 NE2226 1.498 2.650 52: CYS80 SG477 0.207 1.984 1.570 52: Linking CYS-25 SG-14 and CYS-80 SG-477... 52: Marked 447 virtual sites 52: Added 58 dummy masses 52: Added 101 new constraints 52: Before cleaning: 2499 pairs 52: Before cleaning: 2524 dihedrals 52: Using the Oplsaa force field in directory oplsaa.ff 52: 52: going to rename oplsaa.ff/aminoacids.r2b 52: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 52: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 52: 52: Analyzing pdb file 52: Splitting chemical chains based on TER records or chain id changing. 52: 52: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 52: 52: chain #res #atoms 52: 52: 1 'A' 58 488 52: 52: All occupancies are one 52: 52: Reading residue database... (Oplsaa) 52: 52: Processing chain 1 'A' (488 atoms, 58 residues) 52: 52: Identified residue ASN24 as a starting terminus. 52: 52: Identified residue ARG81 as a ending terminus. 52: Start terminus ASN-24: NH3+ 52: End terminus ARG-81: COO- 52: 52: Checking for duplicate atoms.... 52: 52: Generating any missing hydrogen atoms and/or adding termini. 52: 52: Now there are 58 residues with 936 atoms 52: 52: Making bonds... 52: 52: Number of bonds was 951, now 951 52: 52: Generating angles, dihedrals and pairs... 52: 52: Making cmap torsions... 52: 52: There are 2524 dihedrals, 208 impropers, 1704 angles 52: 2469 pairs, 951 bonds and 462 virtual sites 52: 52: Total mass 6908.578 a.m.u. 52: 52: Total charge -6.000 e 52: 52: Writing topology 52: 52: Writing coordinate file... 52: 52: --------- PLEASE NOTE ------------ 52: 52: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 52: 52: The Oplsaa force field and the tip5p water model are used. 52: 52: --------- ETON ESAELP ------------ 52: [ OK ] Oplsaa/Pdb2gmxTest.Runs/ff_oplsaa_tip5p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (112 ms) 52: [----------] 30 tests from Oplsaa/Pdb2gmxTest (2214 ms total) 52: 52: [----------] Global test environment tear-down 52: [==========] 30 tests from 1 test suite ran. (2214 ms total) 52: [ PASSED ] 30 tests. 52/91 Test #52: Pdb2gmx1Test ................................. Passed 2.33 sec test 53 Start 53: Pdb2gmx2Test 53: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pdb2gmx2-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Pdb2gmx2Test.xml" 53: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 53: Test timeout computed to be: 1920 53: [==========] Running 40 tests from 2 test suites. 53: [----------] Global test environment set-up. 53: [----------] 20 tests from G43a1/Pdb2gmxTest 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (64 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (66 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (68 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (60 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (129 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (61 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (71 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (61 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (69 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (158 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (100 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (102 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (64 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (63 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (156 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 37 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 305 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 165 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 172, now 167 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 77 impropers, 241 angles 53: 267 pairs, 167 bonds and 37 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (65 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 53 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 429 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 202 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 216, now 211 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 134 impropers, 316 angles 53: 273 pairs, 211 bonds and 51 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (99 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 36 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 349 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 168 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 179, now 174 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 102 impropers, 260 angles 53: 242 pairs, 174 bonds and 36 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (77 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 33 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 299 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 150 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 159, now 154 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 80 impropers, 227 angles 53: 232 pairs, 154 bonds and 31 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge 0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (81 ms) 53: [ RUN ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.rtp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos43a1.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 146 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1256 dihedrals 53: Using the Gromos43a1 force field in directory gromos43a1.ff 53: 53: going to rename gromos43a1.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos43a1) 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 635 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 655, now 650 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 350 impropers, 955 angles 53: 972 pairs, 650 bonds and 137 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos43a1 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G43a1/Pdb2gmxTest.Runs/ff_gromos43a1_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (185 ms) 53: [----------] 20 tests from G43a1/Pdb2gmxTest (1827 ms total) 53: 53: [----------] 20 tests from G53a6/Pdb2gmxTest 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (74 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (48 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (42 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (55 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (42 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (41 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (43 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spc water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spc_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (87 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 0 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (42 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 0 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (52 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 0 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (43 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 0 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (42 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 0 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (130 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 25 donors and 23 acceptors were found. 53: There are 41 hydrogen bonds 53: Will use HISE for residue 8 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS3 HIS8 53: SG9 NE251 53: HIS8 NE251 1.055 53: MET12 SD83 0.763 0.990 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 39 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 267 pairs 53: Before cleaning: 312 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 53: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 128 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (128 atoms, 16 residues) 53: 53: Identified residue ALA2 as a starting terminus. 53: 53: Identified residue SER17 as a ending terminus. 53: Start terminus ALA-2: NH3+ 53: End terminus SER-17: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 167 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 174, now 169 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 90 dihedrals, 79 impropers, 245 angles 53: 267 pairs, 169 bonds and 39 virtual sites 53: 53: Total mass 1846.116 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (83 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 30 donors and 22 acceptors were found. 53: There are 36 hydrogen bonds 53: Will use HISE for residue 29 53: Will use HISE for residue 32 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS27 HIS29 53: SG90 NE2111 53: HIS29 NE2111 0.987 53: HIS32 NE2135 1.590 1.155 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 57 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 273 pairs 53: Before cleaning: 443 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 53: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 149 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (149 atoms, 16 residues) 53: 53: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue THR18 as a starting terminus. 53: 53: Identified residue PHE33 as a ending terminus. 53: Start terminus THR-18: NH3+ 53: End terminus PHE-33: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 206 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 220, now 215 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 93 dihedrals, 138 impropers, 324 angles 53: 273 pairs, 215 bonds and 55 virtual sites 53: 53: Total mass 2088.361 a.m.u. 53: 53: Total charge 1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (89 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 22 acceptors were found. 53: There are 26 hydrogen bonds 53: Will use HISE for residue 45 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS45 53: NE295 53: MET46 SD102 1.078 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 38 virtual sites 53: Added 4 dummy masses 53: Added 8 new constraints 53: 53: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 242 pairs 53: Before cleaning: 356 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 53: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 132 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (132 atoms, 16 residues) 53: 53: Identified residue ALA34 as a starting terminus. 53: 53: Identified residue ALA49 as a ending terminus. 53: Start terminus ALA-34: NH3+ 53: End terminus ALA-49: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 170 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 181, now 176 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 81 dihedrals, 104 impropers, 264 angles 53: 242 pairs, 176 bonds and 38 virtual sites 53: 53: Total mass 1861.132 a.m.u. 53: 53: Total charge -1.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (55 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 22 donors and 21 acceptors were found. 53: There are 30 hydrogen bonds 53: Will use HISE for residue 60 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: HIS60 53: NE285 53: CYS62 SG98 0.803 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 35 virtual sites 53: Added 4 dummy masses 53: Added 10 new constraints 53: 53: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 232 pairs 53: Before cleaning: 306 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 53: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 53: 53: chain #res #atoms 53: 53: 1 ' ' 16 117 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 (117 atoms, 16 residues) 53: 53: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 53: 53: Identified residue LYS50 as a starting terminus. 53: 53: Identified residue PRO65 as a ending terminus. 53: Start terminus LYS-50: NH3+ 53: End terminus PRO-65: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 16 residues with 152 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 161, now 156 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 78 dihedrals, 82 impropers, 231 angles 53: 232 pairs, 156 bonds and 33 virtual sites 53: 53: Total mass 1662.887 a.m.u. 53: 53: Total charge -0.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (47 ms) 53: [ RUN ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.r2b 53: All occupancies are one 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/atomtypes.atp 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.rtp 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.hdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.n.tdb 53: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/gromos53a6.ff/aminoacids.c.tdb 53: Analysing hydrogen-bonding network for automated assignment of histidine 53: protonation. 89 donors and 98 acceptors were found. 53: There are 129 hydrogen bonds 53: Will use HISE for residue 31 53: Will use HISE for residue 51 53: 9 out of 9 lines of specbond.dat converted successfully 53: Special Atom Distance matrix: 53: CYS25 HIS31 HIS51 53: SG14 NE264 NE2226 53: HIS31 NE264 1.921 53: HIS51 NE2226 1.498 2.650 53: CYS80 SG477 0.207 1.984 1.570 53: Linking CYS-25 SG-14 and CYS-80 SG-477... 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: 53: WARNING: Duplicate line found in or between hackblock and rtp entries 53: 53: Marked 150 virtual sites 53: Added 10 dummy masses 53: Added 29 new constraints 53: 53: WARNING: WARNING: Residue 1 named ASN of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom H used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: 53: WARNING: WARNING: Residue 58 named ARG of a molecule in the input file was mapped 53: to an entry in the topology database, but the atom O used in 53: an interaction of type angle in that entry is not found in the 53: input file. Perhaps your atom and/or residue naming needs to be 53: fixed. 53: 53: 53: Before cleaning: 972 pairs 53: Before cleaning: 1270 dihedrals 53: Using the Gromos53a6 force field in directory gromos53a6.ff 53: 53: going to rename gromos53a6.ff/aminoacids.r2b 53: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 53: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 53: 53: Analyzing pdb file 53: Splitting chemical chains based on TER records or chain id changing. 53: 53: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 53: 53: chain #res #atoms 53: 53: 1 'A' 58 488 53: 53: All occupancies are one 53: 53: Reading residue database... (Gromos53a6) 53: 53: Using default: not generating all possible dihedrals 53: 53: Using default: excluding 3 bonded neighbors 53: 53: Using default: generating 1,4 H--H interactions 53: 53: Using default: removing proper dihedrals found on the same bond as a proper dihedral 53: 53: Processing chain 1 'A' (488 atoms, 58 residues) 53: 53: Identified residue ASN24 as a starting terminus. 53: 53: Identified residue ARG81 as a ending terminus. 53: Start terminus ASN-24: NH3+ 53: End terminus ARG-81: COO- 53: 53: Checking for duplicate atoms.... 53: 53: Generating any missing hydrogen atoms and/or adding termini. 53: 53: Now there are 58 residues with 639 atoms 53: 53: Making bonds... 53: 53: Number of bonds was 659, now 654 53: 53: Generating angles, dihedrals and pairs... 53: 53: Making cmap torsions... 53: 53: There are 321 dihedrals, 354 impropers, 963 angles 53: 972 pairs, 654 bonds and 141 virtual sites 53: 53: Total mass 6908.582 a.m.u. 53: 53: Total charge -6.000 e 53: 53: Writing topology 53: 53: Writing coordinate file... 53: 53: --------- PLEASE NOTE ------------ 53: 53: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 53: 53: The Gromos53a6 force field and the spce water model are used. 53: 53: --------- ETON ESAELP ------------ 53: [ OK ] G53a6/Pdb2gmxTest.Runs/ff_gromos53a6_spce_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (148 ms) 53: [----------] 20 tests from G53a6/Pdb2gmxTest (1268 ms total) 53: 53: [----------] Global test environment tear-down 53: [==========] 40 tests from 2 test suites ran. (3096 ms total) 53: [ PASSED ] 40 tests. 53/91 Test #53: Pdb2gmx2Test ................................. Passed 3.30 sec test 54 Start 54: Pdb2gmx3Test 54: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/pdb2gmx3-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Pdb2gmx3Test.xml" 54: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/gmxpreprocess/tests 54: Test timeout computed to be: 1920 54: [==========] Running 39 tests from 6 test suites. 54: [----------] Global test environment set-up. 54: [----------] 10 tests from Amber/Pdb2gmxTest 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (76 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (85 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (72 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (47 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (120 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 691 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 255, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 691 dihedrals, 51 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.132 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (45 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 788 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 291, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 788 dihedrals, 72 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.366 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (58 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 727 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 262, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 727 dihedrals, 56 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.124 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (45 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 634 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 233, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 634 dihedrals, 48 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.888 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (52 ms) 54: [ RUN ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2631 dihedrals 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 952, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2631 dihedrals, 208 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.576 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Amber99sb-ildn force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Amber/Pdb2gmxTest.Runs/ff_amber99sbildn_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (124 ms) 54: [----------] 10 tests from Amber/Pdb2gmxTest (727 ms total) 54: 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest 54: [ RUN ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/amber99sb-ildn.ff/rna.arn 54: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 54: 54: going to rename amber99sb-ildn.ff/aminoacids.r2b 54: 54: going to rename amber99sb-ildn.ff/dna.r2b 54: 54: going to rename amber99sb-ildn.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb... 54: Read 'TIP4p ice to test that MW is handled correctly', 4 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 0 chains and 1 blocks of water and 2 residues with 4 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 2 4 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Amber99sb-ildn) 54: 54: Processing chain 1 (4 atoms, 2 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 2 residues with 8 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4, now 4 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 2 angles 54: 0 pairs, 4 bonds and 0 virtual sites 54: 54: Total mass 36.032 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/tip4p.pdb. 54: 54: The Amber99sb-ildn force field and the tip4p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] AmberTip4p/Pdb2gmxTest.Runs/ff_amber99sbildn_tip4p_vsite_none_id_or_ter_merge_no_tip4ppdb_format_gro_match_full (23 ms) 54: [----------] 1 test from AmberTip4p/Pdb2gmxTest (23 ms total) 54: 54: [----------] 12 tests from Charmm/Pdb2gmxTest 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 0 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Apdb_format_gro_match_file (43 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 0 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Bpdb_format_gro_match_file (45 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 0 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Cpdb_format_gro_match_file (34 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 0 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Dpdb_format_gro_match_file (32 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 0 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_Epdb_format_gro_match_file (86 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 0 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_monomerpdb_format_gro_match_file (17 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 124 virtual sites 54: Added 16 dummy masses 54: Added 26 new constraints 54: Before cleaning: 653 pairs 54: Before cleaning: 663 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 128 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (128 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 252 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 254, now 254 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 663 dihedrals, 48 impropers, 457 angles 54: 650 pairs, 254 bonds and 130 virtual sites 54: 54: Total mass 1846.115 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/A.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Apdb_format_gro_match_file (129 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 30 donors and 22 acceptors were found. 54: There are 36 hydrogen bonds 54: Will use HISE for residue 29 54: Will use HISE for residue 32 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS27 HIS29 54: SG90 NE2111 54: HIS29 NE2111 0.987 54: HIS32 NE2135 1.590 1.155 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 132 virtual sites 54: Added 10 dummy masses 54: Added 19 new constraints 54: Before cleaning: 748 pairs 54: Before cleaning: 778 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb... 54: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 149 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (149 atoms, 16 residues) 54: 54: Replaced 1 residue named GLUH to the default GLU. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue PHE33 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus PHE-33: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 281 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 290, now 290 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 778 dihedrals, 49 impropers, 516 angles 54: 736 pairs, 290 bonds and 133 virtual sites 54: 54: Total mass 2088.361 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/B.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Bpdb_format_gro_match_file (124 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 22 acceptors were found. 54: There are 26 hydrogen bonds 54: Will use HISE for residue 45 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS45 54: NE295 54: MET46 SD102 1.078 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 123 virtual sites 54: Added 22 dummy masses 54: Added 35 new constraints 54: Before cleaning: 676 pairs 54: Before cleaning: 696 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb... 54: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 132 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (132 atoms, 16 residues) 54: 54: Identified residue ALA34 as a starting terminus. 54: 54: Identified residue ALA49 as a ending terminus. 54: Start terminus ALA-34: NH3+ 54: End terminus ALA-49: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 261, now 261 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 696 dihedrals, 39 impropers, 472 angles 54: 667 pairs, 261 bonds and 132 virtual sites 54: 54: Total mass 1861.130 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/C.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Cpdb_format_gro_match_file (86 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 22 donors and 21 acceptors were found. 54: There are 30 hydrogen bonds 54: Will use HISE for residue 60 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS60 54: NE285 54: CYS62 SG98 0.803 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 111 virtual sites 54: Added 18 dummy masses 54: Added 31 new constraints 54: Before cleaning: 603 pairs 54: Before cleaning: 618 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb... 54: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 54: 54: chain #res #atoms 54: 54: 1 ' ' 16 117 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 (117 atoms, 16 residues) 54: 54: Replaced 1 residue named ASPH to the default ASP. Use interactive selection of protonated residues if that is what you need. 54: 54: Identified residue LYS50 as a starting terminus. 54: 54: Identified residue PRO65 as a ending terminus. 54: Start terminus LYS-50: NH3+ 54: End terminus PRO-65: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 228 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 232, now 232 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 14 cmap torsion pairs 54: 54: There are 618 dihedrals, 38 impropers, 419 angles 54: 597 pairs, 232 bonds and 116 virtual sites 54: 54: Total mass 1662.885 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/D.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Dpdb_format_gro_match_file (73 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 89 donors and 98 acceptors were found. 54: There are 129 hydrogen bonds 54: Will use HISE for residue 31 54: Will use HISE for residue 51 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS25 HIS31 HIS51 54: SG14 NE264 NE2226 54: HIS31 NE264 1.921 54: HIS51 NE2226 1.498 2.650 54: CYS80 SG477 0.207 1.984 1.570 54: Linking CYS-25 SG-14 and CYS-80 SG-477... 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 447 virtual sites 54: Added 58 dummy masses 54: Added 101 new constraints 54: Before cleaning: 2499 pairs 54: Before cleaning: 2524 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb... 54: Read 'This is a fragment of 2d4f for testing a disulfide bridge', 488 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 58 residues with 488 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 58 488 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (488 atoms, 58 residues) 54: 54: Identified residue ASN24 as a starting terminus. 54: 54: Identified residue ARG81 as a ending terminus. 54: Start terminus ASN-24: NH3+ 54: End terminus ARG-81: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 58 residues with 936 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 951, now 951 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 56 cmap torsion pairs 54: 54: There are 2524 dihedrals, 149 impropers, 1704 angles 54: 2469 pairs, 951 bonds and 462 virtual sites 54: 54: Total mass 6908.566 a.m.u. 54: 54: Total charge -6.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/E.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_Epdb_format_gro_match_file (194 ms) 54: [ RUN ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Marked 8 virtual sites 54: Added 2 dummy masses 54: Added 3 new constraints 54: Before cleaning: 39 pairs 54: Before cleaning: 39 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb... 54: Read 'GLU', 9 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 1 residues with 9 atoms 54: 54: chain #res #atoms 54: 54: 1 'X' 1 9 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'X' (9 atoms, 1 residues) 54: 54: Identified residue GLU1 as a starting terminus. 54: 54: Identified residue GLU1 as a ending terminus. 54: Start terminus GLU-1: NH3+ 54: End terminus GLU-1: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 1 residues with 18 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 17, now 17 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 39 dihedrals, 2 impropers, 30 angles 54: 39 pairs, 17 bonds and 9 virtual sites 54: 54: Total mass 146.123 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/monomer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Charmm/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_h_id_or_ter_merge_no_monomerpdb_format_gro_match_file (35 ms) 54: [----------] 12 tests from Charmm/Pdb2gmxTest (903 ms total) 54: 54: [----------] 8 tests from ChainSep/Pdb2gmxTest 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_all_chainTerpdb_format_gro_match_file (89 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 7 acceptors were found. 54: There are 7 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: HIS8 54: NE223 54: MET12 SD55 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 317 pairs 54: Before cleaning: 322 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 7 58 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (58 atoms, 7 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 124 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 125, now 125 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 5 cmap torsion pairs 54: 54: There are 322 dihedrals, 19 impropers, 227 angles 54: 314 pairs, 125 bonds and 0 virtual sites 54: 54: Total mass 846.083 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 124 atoms 7 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_chainTerpdb_format_gro_match_file (63 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 651 pairs 54: Before cleaning: 661 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 258 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 258, now 258 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 10 cmap torsion pairs 54: 54: There are 661 dihedrals, 46 impropers, 463 angles 54: 648 pairs, 258 bonds and 0 virtual sites 54: 54: Total mass 1882.146 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_all_chainTerpdb_format_gro_match_file (69 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 10 donors and 12 acceptors were found. 54: There are 13 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 54: SG9 54: HIS8 NE251 1.055 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 288 pairs 54: Before cleaning: 293 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 8 61 54: 54: 2 'B' 3 25 54: 54: 3 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (61 atoms, 8 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 8 residues with 114 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 115, now 115 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6 cmap torsion pairs 54: 54: There are 293 dihedrals, 23 impropers, 203 angles 54: 285 pairs, 115 bonds and 0 virtual sites 54: 54: Total mass 888.952 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 114 atoms 8 residues 54: 54: Including chain 2 in system: 61 atoms 3 residues 54: 54: Including chain 3 in system: 83 atoms 5 residues 54: 54: Now there are 258 atoms and 16 residues 54: 54: Total mass in system 1882.146 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_chainTerpdb_format_gro_match_file (66 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 650 pairs 54: Before cleaning: 660 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Merged chains into joint molecule definitions at 3 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 261 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 260, now 260 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 8 cmap torsion pairs 54: 54: There are 660 dihedrals, 45 impropers, 466 angles 54: 647 pairs, 260 bonds and 0 virtual sites 54: 54: Total mass 1900.162 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_chainTerpdb_format_gro_match_file (69 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 123 pairs 54: Before cleaning: 123 dihedrals 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 6 donors and 4 acceptors were found. 54: There are 3 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 164 pairs 54: Before cleaning: 169 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 152 pairs 54: Before cleaning: 152 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'B' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 4 28 54: 54: 2 'B' 4 33 54: 54: 3 'B' 3 25 54: 54: 4 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (28 atoms, 4 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue GLU5 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus GLU-5: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 51 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 50, now 50 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 123 dihedrals, 9 impropers, 88 angles 54: 123 pairs, 50 bonds and 0 virtual sites 54: 54: Total mass 434.421 a.m.u. 54: 54: Total charge -2.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (33 atoms, 4 residues) 54: 54: Identified residue PHE6 as a starting terminus. 54: 54: Identified residue ILE9 as a ending terminus. 54: Start terminus PHE-6: NH3+ 54: End terminus ILE-9: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 4 residues with 66 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 67, now 67 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 2 cmap torsion pairs 54: 54: There are 169 dihedrals, 13 impropers, 118 angles 54: 161 pairs, 67 bonds and 0 virtual sites 54: 54: Total mass 472.547 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'B' (25 atoms, 3 residues) 54: 54: Identified residue LYS10 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus LYS-10: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 61 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 60, now 60 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 152 dihedrals, 5 impropers, 112 angles 54: 152 pairs, 60 bonds and 0 virtual sites 54: 54: Total mass 391.552 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Processing chain 4 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 51 atoms 4 residues 54: 54: Including chain 2 in system: 66 atoms 4 residues 54: 54: Including chain 3 in system: 61 atoms 3 residues 54: 54: Including chain 4 in system: 83 atoms 5 residues 54: 54: Now there are 261 atoms and 16 residues 54: 54: Total mass in system 1900.162 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_chainTerpdb_format_gro_match_file (67 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 25 donors and 23 acceptors were found. 54: There are 41 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 652 pairs 54: Before cleaning: 662 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: Merged chains into joint molecule definitions at 1 places. 54: 54: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 16 127 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (127 atoms, 16 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 255 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 256, now 256 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 12 cmap torsion pairs 54: 54: There are 662 dihedrals, 47 impropers, 460 angles 54: 649 pairs, 256 bonds and 0 virtual sites 54: 54: Total mass 1864.131 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_all_chainTerpdb_format_gro_match_file (69 ms) 54: [ RUN ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: Analysing hydrogen-bonding network for automated assignment of histidine 54: protonation. 14 donors and 15 acceptors were found. 54: There are 20 hydrogen bonds 54: Will use HISE for residue 8 54: 9 out of 9 lines of specbond.dat converted successfully 54: Special Atom Distance matrix: 54: CYS3 HIS8 54: SG9 NE251 54: HIS8 NE251 1.055 54: MET12 SD83 0.763 0.990 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 441 pairs 54: Before cleaning: 446 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 211 pairs 54: Before cleaning: 216 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 54: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 11 86 54: 54: 2 'C' 5 41 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (86 atoms, 11 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue MET12 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus MET-12: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 11 residues with 172 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 173, now 173 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 9 cmap torsion pairs 54: 54: There are 446 dihedrals, 29 impropers, 312 angles 54: 438 pairs, 173 bonds and 0 virtual sites 54: 54: Total mass 1262.488 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'C' (41 atoms, 5 residues) 54: 54: Identified residue ASN13 as a starting terminus. 54: 54: Identified residue SER17 as a ending terminus. 54: Start terminus ASN-13: NH3+ 54: End terminus SER-17: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 5 residues with 83 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 83, now 83 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 3 cmap torsion pairs 54: 54: There are 216 dihedrals, 18 impropers, 148 angles 54: 211 pairs, 83 bonds and 0 virtual sites 54: 54: Total mass 601.643 a.m.u. 54: 54: Total charge 1.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 172 atoms 11 residues 54: 54: Including chain 2 in system: 83 atoms 5 residues 54: 54: Now there are 255 atoms and 16 residues 54: 54: Total mass in system 1864.131 a.m.u. 54: 54: Total charge in system 0.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainSep/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_chainTerpdb_format_gro_match_file (50 ms) 54: [----------] 8 tests from ChainSep/Pdb2gmxTest (547 ms total) 54: 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on changing chain id only (ignoring TER records). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_merge_no_fragmentspdb_format_pdb_match_file (45 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records only (ignoring chain id). 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_ter_merge_no_fragmentspdb_format_pdb_match_file (29 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_fragmentspdb_format_pdb_match_file (25 ms) 54: [ RUN ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 83 pairs 54: Before cleaning: 83 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 145 pairs 54: Before cleaning: 150 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb... 54: Read 'Fragments of peptides and ions', 47 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records and chain id changing. 54: 54: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 3 19 54: 54: 2 'B' 3 28 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (19 atoms, 3 residues) 54: 54: Identified residue ALA2 as a starting terminus. 54: 54: Identified residue ASP4 as a ending terminus. 54: Start terminus ALA-2: NH3+ 54: End terminus ASP-4: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 36 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 35, now 35 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 83 dihedrals, 6 impropers, 61 angles 54: 83 pairs, 35 bonds and 0 virtual sites 54: 54: Total mass 306.314 a.m.u. 54: 54: Total charge -1.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'B' (28 atoms, 3 residues) 54: 54: Identified residue THR18 as a starting terminus. 54: 54: Identified residue TRP20 as a ending terminus. 54: Start terminus THR-18: NH3+ 54: End terminus TRP-20: COO- 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 3 residues with 57 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 58, now 58 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 1 cmap torsion pairs 54: 54: There are 150 dihedrals, 5 impropers, 103 angles 54: 142 pairs, 58 bonds and 0 virtual sites 54: 54: Total mass 404.468 a.m.u. 54: 54: Total charge -0.000 e 54: 54: Writing topology 54: 54: Including chain 1 in system: 36 atoms 3 residues 54: 54: Including chain 2 in system: 57 atoms 3 residues 54: 54: Now there are 93 atoms and 6 residues 54: 54: Total mass in system 710.782 a.m.u. 54: 54: Total charge in system -1.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/fragments.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] ChainChanges/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_and_ter_merge_no_fragmentspdb_format_pdb_match_file (29 ms) 54: [----------] 4 tests from ChainChanges/Pdb2gmxTest (130 ms total) 54: 54: [----------] 4 tests from Cyclic/Pdb2gmxTest 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 6040 pairs 54: Before cleaning: 6605 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Chain identifier 'Q' is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file. 54: 54: Moved all the water blocks to the end 54: 54: There are 3 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 71 1527 54: 54: 2 'Q' 71 1527 54: 54: 3 'Q' 7 7 54: 54: 4 ' ' 10 10 (only water) 54: 54: 5 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 2 'Q' (1527 atoms, 71 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 71 residues with 2297 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: Number of bonds was 2481, now 2481 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 6605 dihedrals, 183 impropers, 4434 angles 54: 5827 pairs, 2481 bonds and 0 virtual sites 54: 54: Total mass 22984.514 a.m.u. 54: 54: Total charge -71.000 e 54: 54: Writing topology 54: 54: Processing chain 3 'Q' (7 atoms, 7 residues) 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 7 residues with 7 atoms 54: Chain time... 54: 54: Making bonds... 54: 54: No bonds 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 0 angles 54: 0 pairs, 0 bonds and 0 virtual sites 54: 54: Total mass 170.135 a.m.u. 54: 54: Total charge 14.000 e 54: 54: Writing topology 54: 54: Processing chain 4 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 5 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 2297 atoms 71 residues 54: 54: Including chain 2 in system: 2297 atoms 71 residues 54: 54: Including chain 3 in system: 7 atoms 7 residues 54: 54: Including chain 4 in system: 30 atoms 10 residues 54: 54: Including chain 5 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.562 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycrnapdb_format_gro_match_file (384 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_no_cycprotpdb_format_gro_match_file (98 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: WARNING: all CONECT records are ignored 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 12080 pairs 54: Before cleaning: 13210 dihedrals 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb... 54: Read 'L1 RIBOZYME RNA LIGASE', 3087 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: Moved all the water blocks to the end 54: 54: Merged chains into joint molecule definitions at 2 places. 54: 54: There are 1 chains and 2 blocks of water and 175 residues with 3087 atoms 54: 54: chain #res #atoms 54: 54: 1 'P' 149 3061 54: 54: 2 ' ' 10 10 (only water) 54: 54: 3 ' ' 16 16 (only water) 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'P' (3061 atoms, 149 residues) 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Identified residue G1 as a starting terminus. 54: 54: Identified residue U71 as a ending terminus. 54: 54: Residue MG72 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG73 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG74 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG75 has type 'Ion', assuming it is not linked into a chain. 54: 54: Residue MG76 has type 'Ion', assuming it is not linked into a chain. 54: 54: Disabling further notes about ions. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 149 residues with 4601 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 4962, now 4962 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 13210 dihedrals, 366 impropers, 8868 angles 54: 11654 pairs, 4962 bonds and 0 virtual sites 54: 54: Total mass 46139.162 a.m.u. 54: 54: Total charge -128.000 e 54: 54: Writing topology 54: 54: Processing chain 2 (10 atoms, 10 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 10 residues with 30 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 30, now 30 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 30 angles 54: 0 pairs, 30 bonds and 0 virtual sites 54: 54: Total mass 180.154 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Processing chain 3 (16 atoms, 16 residues) 54: 54: Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 16 residues with 48 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 48, now 48 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 0 dihedrals, 0 impropers, 48 angles 54: 0 pairs, 48 bonds and 0 virtual sites 54: 54: Total mass 288.246 a.m.u. 54: 54: Total charge 0.000 e 54: 54: Including chain 1 in system: 4601 atoms 149 residues 54: 54: Including chain 2 in system: 30 atoms 10 residues 54: 54: Including chain 3 in system: 48 atoms 16 residues 54: 54: Now there are 4679 atoms and 175 residues 54: 54: Total mass in system 46607.562 a.m.u. 54: 54: Total charge in system -128.000 e 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-rna.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycrnapdb_format_gro_match_file (750 ms) 54: [ RUN ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.r2b 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.r2b 54: All occupancies are one 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/atomtypes.atp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.rtp 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/lipids.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.hdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.n.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.c.tdb 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.c.tdb 54: 9 out of 9 lines of specbond.dat converted successfully 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/aminoacids.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/dna.arn 54: Opening force field file /build/reproducible-path/gromacs-2024.4/share/top/charmm27.ff/rna.arn 54: Before cleaning: 2325 pairs 54: Before cleaning: 2325 dihedrals 54: Using the Charmm27 force field in directory charmm27.ff 54: 54: going to rename charmm27.ff/aminoacids.r2b 54: 54: going to rename charmm27.ff/rna.r2b 54: Reading /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb... 54: Read 'CARNOCYCLIN-A', 413 atoms 54: 54: Analyzing pdb file 54: Splitting chemical chains based on TER records or chain id changing. 54: 54: There are 1 chains and 0 blocks of water and 60 residues with 413 atoms 54: 54: chain #res #atoms 54: 54: 1 'A' 60 413 54: 54: All occupancies are one 54: 54: Reading residue database... (Charmm27) 54: 54: Processing chain 1 'A' (413 atoms, 60 residues) 54: 54: Identified residue LEU1 as a starting terminus. 54: 54: Identified residue LEU60 as a ending terminus. 54: 54: Checking for duplicate atoms.... 54: 54: Generating any missing hydrogen atoms and/or adding termini. 54: 54: Now there are 60 residues with 878 atoms 54: 54: Making bonds... 54: 54: Number of bonds was 880, now 880 54: 54: Generating angles, dihedrals and pairs... 54: 54: Making cmap torsions... 54: 54: There are 60 cmap torsion pairs 54: 54: There are 2325 dihedrals, 137 impropers, 1614 angles 54: 2319 pairs, 880 bonds and 0 virtual sites 54: 54: Total mass 5866.087 a.m.u. 54: 54: Total charge 4.000 e 54: 54: Writing topology 54: 54: Writing coordinate file... 54: 54: --------- PLEASE NOTE ------------ 54: 54: You have successfully generated a topology from: /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/cyc-prot.pdb. 54: 54: The Charmm27 force field and the tip3p water model are used. 54: 54: --------- ETON ESAELP ------------ 54: [ OK ] Cyclic/Pdb2gmxTest.Runs/ff_charmm27_tip3p_vsite_none_id_or_ter_merge_all_cycprotpdb_format_gro_match_file (101 ms) 54: [----------] 4 tests from Cyclic/Pdb2gmxTest (1334 ms total) 54: 54: [----------] Global test environment tear-down 54: [==========] 39 tests from 6 test suites ran. (3667 ms total) 54: [ PASSED ] 39 tests. 54/91 Test #54: Pdb2gmx3Test ................................. Passed 3.85 sec test 55 Start 55: CorrelationsTest 55: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/correlations-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/CorrelationsTest.xml" 55: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/correlationfunctions/tests 55: Test timeout computed to be: 30 55: [==========] Running 21 tests from 3 test suites. 55: [----------] Global test environment set-up. 55: [----------] 10 tests from AutocorrTest 55: [ RUN ] AutocorrTest.EacNormal 55: [ OK ] AutocorrTest.EacNormal (60 ms) 55: [ RUN ] AutocorrTest.EacNoNormalize 55: [ OK ] AutocorrTest.EacNoNormalize (48 ms) 55: [ RUN ] AutocorrTest.EacCos 55: [ OK ] AutocorrTest.EacCos (50 ms) 55: [ RUN ] AutocorrTest.EacVector 55: [ OK ] AutocorrTest.EacVector (45 ms) 55: [ RUN ] AutocorrTest.EacRcross 55: [ OK ] AutocorrTest.EacRcross (0 ms) 55: [ RUN ] AutocorrTest.EacP0 55: [ OK ] AutocorrTest.EacP0 (49 ms) 55: [ RUN ] AutocorrTest.EacP1 55: [ OK ] AutocorrTest.EacP1 (47 ms) 55: [ RUN ] AutocorrTest.EacP2 55: [ OK ] AutocorrTest.EacP2 (66 ms) 55: [ RUN ] AutocorrTest.EacP3 55: [ OK ] AutocorrTest.EacP3 (1 ms) 55: [ RUN ] AutocorrTest.EacP4 55: [ OK ] AutocorrTest.EacP4 (34 ms) 55: [----------] 10 tests from AutocorrTest (407 ms total) 55: 55: [----------] 10 tests from ExpfitTest 55: [ RUN ] ExpfitTest.EffnEXP1 55: [ OK ] ExpfitTest.EffnEXP1 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP2 55: [ OK ] ExpfitTest.EffnEXP2 (0 ms) 55: [ RUN ] ExpfitTest.EffnEXPEXP 55: [ OK ] ExpfitTest.EffnEXPEXP (0 ms) 55: [ RUN ] ExpfitTest.EffnEXP5 55: [ OK ] ExpfitTest.EffnEXP5 (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP7 55: [ OK ] ExpfitTest.EffnEXP7 (1 ms) 55: [ RUN ] ExpfitTest.EffnEXP9 55: [ OK ] ExpfitTest.EffnEXP9 (19 ms) 55: [ RUN ] ExpfitTest.EffnERF 55: [ OK ] ExpfitTest.EffnERF (1 ms) 55: [ RUN ] ExpfitTest.EffnERREST 55: [ OK ] ExpfitTest.EffnERREST (9 ms) 55: [ RUN ] ExpfitTest.EffnVAC 55: [ OK ] ExpfitTest.EffnVAC (3 ms) 55: [ RUN ] ExpfitTest.EffnPRES 55: [ OK ] ExpfitTest.EffnPRES (11 ms) 55: [----------] 10 tests from ExpfitTest (48 ms total) 55: 55: [----------] 1 test from ManyAutocorrelationTest 55: [ RUN ] ManyAutocorrelationTest.Empty 55: [ OK ] ManyAutocorrelationTest.Empty (0 ms) 55: [----------] 1 test from ManyAutocorrelationTest (0 ms total) 55: 55: [----------] Global test environment tear-down 55: [==========] 21 tests from 3 test suites ran. (467 ms total) 55: [ PASSED ] 21 tests. 55/91 Test #55: CorrelationsTest ............................. Passed 0.61 sec test 56 Start 56: AnalysisDataUnitTests 56: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/analysisdata-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/AnalysisDataUnitTests.xml" 56: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/analysisdata/tests 56: Test timeout computed to be: 30 56: [==========] Running 69 tests from 14 test suites. 56: [----------] Global test environment set-up. 56: [----------] 3 tests from AnalysisDataInitializationTest 56: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 56: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 56: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 56: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 56: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/0 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/1 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/2 (1 ms total) 56: 56: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 56: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 56: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 56: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (0 ms) 56: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 56: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (0 ms) 56: [----------] 8 tests from AnalysisDataCommonTest/3 (1 ms total) 56: 56: [----------] 4 tests from AnalysisArrayDataTest 56: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 56: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (0 ms) 56: [ RUN ] AnalysisArrayDataTest.StorageWorks 56: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 56: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 56: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 56: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 56: [----------] 4 tests from AnalysisArrayDataTest (0 ms total) 56: 56: [----------] 6 tests from AverageModuleTest 56: [ RUN ] AverageModuleTest.BasicTest 56: [ OK ] AverageModuleTest.BasicTest (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipointData 56: [ OK ] AverageModuleTest.HandlesMultipointData (0 ms) 56: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 56: [ OK ] AverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 56: [ OK ] AverageModuleTest.HandlesDataSetAveraging (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeXAxis 56: [ OK ] AverageModuleTest.CanCustomizeXAxis (0 ms) 56: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 56: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (0 ms) 56: [----------] 6 tests from AverageModuleTest (1 ms total) 56: 56: [----------] 2 tests from FrameAverageModuleTest 56: [ RUN ] FrameAverageModuleTest.BasicTest 56: [ OK ] FrameAverageModuleTest.BasicTest (0 ms) 56: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 2 tests from FrameAverageModuleTest (0 ms total) 56: 56: [----------] 7 tests from AnalysisHistogramSettingsTest 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 56: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 56: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 56: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 56: 56: [----------] 2 tests from SimpleHistogramModuleTest 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (12 ms) 56: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [----------] 2 tests from SimpleHistogramModuleTest (13 ms total) 56: 56: [----------] 3 tests from WeightedHistogramModuleTest 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 56: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 56: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from WeightedHistogramModuleTest (1 ms total) 56: 56: [----------] 3 tests from BinAverageModuleTest 56: [ RUN ] BinAverageModuleTest.ComputesCorrectly 56: [ OK ] BinAverageModuleTest.ComputesCorrectly (0 ms) 56: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 56: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (0 ms) 56: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 56: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from BinAverageModuleTest (0 ms total) 56: 56: [----------] 4 tests from AbstractAverageHistogramTest 56: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 56: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 56: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (0 ms) 56: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 56: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (0 ms) 56: [----------] 4 tests from AbstractAverageHistogramTest (1 ms total) 56: 56: [----------] 3 tests from LifetimeModuleTest 56: [ RUN ] LifetimeModuleTest.BasicTest 56: [ OK ] LifetimeModuleTest.BasicTest (0 ms) 56: [ RUN ] LifetimeModuleTest.CumulativeTest 56: [ OK ] LifetimeModuleTest.CumulativeTest (0 ms) 56: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 56: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (0 ms) 56: [----------] 3 tests from LifetimeModuleTest (0 ms total) 56: 56: [----------] Global test environment tear-down 56: [==========] 69 tests from 14 test suites ran. (26 ms total) 56: [ PASSED ] 69 tests. 56/91 Test #56: AnalysisDataUnitTests ........................ Passed 0.16 sec test 57 Start 57: CoordinateIOTests 57: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/coordinateio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/CoordinateIOTests.xml" 57: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/coordinateio/tests 57: Test timeout computed to be: 30 57: [==========] Running 67 tests from 20 test suites. 57: [----------] Global test environment set-up. 57: [----------] 1 test from OutputSelectorDeathTest 57: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (5 ms) 57: [----------] 1 test from OutputSelectorDeathTest (5 ms total) 57: 57: [----------] 5 tests from TrajectoryFrameWriterTest 57: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (1 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (0 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (0 ms) 57: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (5 ms) 57: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks 57: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms) 57: [----------] 5 tests from TrajectoryFrameWriterTest (8 ms total) 57: 57: [----------] 5 tests from OutputAdapterContainer 57: [ RUN ] OutputAdapterContainer.MakeEmpty 57: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms) 57: [ RUN ] OutputAdapterContainer.AddAdapter 57: [ OK ] OutputAdapterContainer.AddAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectBadAdapter 57: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter 57: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms) 57: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters 57: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms) 57: [----------] 5 tests from OutputAdapterContainer (0 ms total) 57: 57: [----------] 3 tests from RegisterFrameConverterTest 57: [ RUN ] RegisterFrameConverterTest.NoConverterWorks 57: [ OK ] RegisterFrameConverterTest.NoConverterWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.RegistrationWorks 57: [ OK ] RegisterFrameConverterTest.RegistrationWorks (0 ms) 57: [ RUN ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees 57: [ OK ] RegisterFrameConverterTest.NewConverterCanInvalidateGuarantees (0 ms) 57: [----------] 3 tests from RegisterFrameConverterTest (0 ms total) 57: 57: [----------] 5 tests from FlagTest 57: [ RUN ] FlagTest.CanSetSimpleFlag 57: [ OK ] FlagTest.CanSetSimpleFlag (0 ms) 57: [ RUN ] FlagTest.CanAddNewBox 57: [ OK ] FlagTest.CanAddNewBox (0 ms) 57: [ RUN ] FlagTest.SetsImplicitPrecisionChange 57: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitStartTimeChange 57: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms) 57: [ RUN ] FlagTest.SetsImplicitTimeStepChange 57: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms) 57: [----------] 5 tests from FlagTest (0 ms total) 57: 57: [----------] 5 tests from SetAtomsTest 57: [ RUN ] SetAtomsTest.RemovesExistingAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.RemovesExistingAtoms (0 ms) 57: [ RUN ] SetAtomsTest.AddsNewAtoms 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.AddsNewAtoms (0 ms) 57: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (5 ms) 57: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (0 ms) 57: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (0 ms) 57: [----------] 5 tests from SetAtomsTest (8 ms total) 57: 57: [----------] 2 tests from SetBothTimeTest 57: [ RUN ] SetBothTimeTest.StartTimeZeroWorks 57: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms) 57: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks 57: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms) 57: [----------] 2 tests from SetBothTimeTest (0 ms total) 57: 57: [----------] 2 tests from SetStartTimeTest 57: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart 57: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms) 57: [ RUN ] SetStartTimeTest.WorksWithZeroStart 57: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms) 57: [----------] 2 tests from SetStartTimeTest (0 ms total) 57: 57: [----------] 1 test from SetTimeStepTest 57: [ RUN ] SetTimeStepTest.SetTimeStepWorks 57: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms) 57: [----------] 1 test from SetTimeStepTest (0 ms total) 57: 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (1 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (0 ms) 57: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (9 ms) 57: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (13 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (2 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (2 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (1 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (10 ms) 57: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (1 ms) 57: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (16 ms total) 57: 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (1 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (2 ms total) 57: 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms) 57: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (0 ms) 57: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (1 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total) 57: 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (13 ms) 57: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (0 ms) 57: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (14 ms total) 57: 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms) 57: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 57: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms) 57: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (0 ms total) 57: 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (0 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (0 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (1 ms) 57: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3 57: 57: WARNING: Masses and atomic (Van der Waals) radii will be guessed 57: based on residue and atom names, since they could not be 57: definitively assigned from the information in your input 57: files. These guessed numbers might deviate from the mass 57: and radius of the atom type. Please check the output 57: files if necessary. Note, that this functionality may 57: be removed in a future GROMACS version. Please, consider 57: using another file format for your input. 57: 57: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (0 ms) 57: [----------] 4 tests from ModuleSupported/NoOptionalOutput (3 ms total) 57: 57: [----------] Global test environment tear-down 57: [==========] 67 tests from 20 test suites ran. (78 ms total) 57: [ PASSED ] 67 tests. 57/91 Test #57: CoordinateIOTests ............................ Passed 0.23 sec test 58 Start 58: TrajectoryAnalysisUnitTests 58: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/trajectoryanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 58: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests 58: Test timeout computed to be: 1920 58: [==========] Running 385 tests from 24 test suites. 58: [----------] Global test environment set-up. 58: [----------] 11 tests from AngleModuleTest 58: [ RUN ] AngleModuleTest.ComputesSimpleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesSimpleAngles (9 ms) 58: [ RUN ] AngleModuleTest.ComputesDihedrals 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesDihedrals (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPairAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (5 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 58: Reading frames from gro file 'Test system for different angles', 33 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (1 ms) 58: [ RUN ] AngleModuleTest.ComputesMultipleAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.ComputesMultipleAngles (9 ms) 58: [ RUN ] AngleModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (1 ms) 58: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (5 ms) 58: [----------] 11 tests from AngleModuleTest (39 ms total) 58: 58: [----------] 5 tests from ClustsizeTest 58: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 2, cmax: 4, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (0 ms) 58: [ RUN ] ClustsizeTest.NoMolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 58: There is one group in the index 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 24 58: cmid: 1, cmax: 6, max_size: 6 58: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 58: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (0 ms) 58: [ RUN ] ClustsizeTest.MolDefaultCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (4 ms) 58: [ RUN ] ClustsizeTest.MolShortCutoff 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 1, cmax: 6, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (1 ms) 58: [ RUN ] ClustsizeTest.MolCSize 58: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Total number of atoms in clusters = 8 58: cmid: 2, cmax: 4, max_size: 2 58: 50%100%cmid: 2, cmax: 6, max_size: 2 58: 50%100%[ OK ] ClustsizeTest.MolCSize (0 ms) 58: [----------] 5 tests from ClustsizeTest (8 ms total) 58: 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (0 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 58: Reading frames from gro file 'Test system', 8 atoms. 58: Reading frame 0 time 0.000 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (5 ms) 58: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 58: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 58: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (7 ms total) 58: 58: [----------] 4 tests from ConvertTrjModuleTest 58: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (14 ms) 58: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (9 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (0 ms) 58: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 24 atoms 58: Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (0 ms) 58: [----------] 4 tests from ConvertTrjModuleTest (26 ms total) 58: 58: [----------] 6 tests from DistanceModuleTest 58: [ RUN ] DistanceModuleTest.ComputesDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: [ OK ] DistanceModuleTest.ComputesDistances (1 ms) 58: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2: 58: Number of samples: 5 58: Average distance: 1.43246 nm 58: Standard deviation: 0.96700 nm 58: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 58: Number of samples: 4 58: Average distance: 1.81066 nm 58: Standard deviation: 0.79289 nm 58: [ OK ] DistanceModuleTest.ComputesMultipleDistances (1 ms) 58: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: atomname S1 S2 and res_cog x < 2.8: 58: Number of samples: 3 58: Average distance: 1.72076 nm 58: Standard deviation: 1.24839 nm 58: [ OK ] DistanceModuleTest.HandlesDynamicSelections (1 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: Contacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroup (6 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: SuccessiveContacts: 58: Number of samples: 2 58: Average distance: 1.00000 nm 58: Standard deviation: 0.00000 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromGroupWithSuccessiveIndices (8 ms) 58: [ RUN ] DistanceModuleTest.HandlesSelectionFromLargeGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: ManyContacts: 58: Number of samples: 10 58: Average distance: 1.82913 nm 58: Standard deviation: 0.78478 nm 58: [ OK ] DistanceModuleTest.HandlesSelectionFromLargeGroup (8 ms) 58: [----------] 6 tests from DistanceModuleTest (35 ms total) 58: 58: [----------] 2 tests from ExtractClusterModuleTest 58: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms 58: trr version: GMX_trn_file (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (5 ms) 58: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset 58: Reading frame 0 time 0.000 Reading frame 1 time 0.002 Reading frame 2 time 0.004 Reading frame 3 time 0.006 Reading frame 4 time 0.008 Reading frame 5 time 0.010 Reading frame 6 time 0.012 Reading frame 7 time 0.014 Reading frame 8 time 0.016 Reading frame 9 time 0.018 Reading frame 10 time 0.020 Reading frame 11 time 0.022 Reading frame 12 time 0.024 Reading frame 13 time 0.026 Reading frame 14 time 0.028 Reading frame 15 time 0.030 Reading frame 16 time 0.032 Reading frame 17 time 0.034 Reading frame 18 time 0.036 Reading frame 19 time 0.038 Reading frame 20 time 0.040 58: Analyzed 26 frames, last time 0.050 58: There are 8 clusters containing 26 structures, highest framenr is 25 58: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (1 ms) 58: [----------] 2 tests from ExtractClusterModuleTest (6 ms total) 58: 58: [----------] 2 tests from FreeVolumeModuleTest 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for CO2-RM. Set to zero. 58: Could not determine VDW radius for 40 particles. These were set to zero. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 13 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 58: van der Spoel and Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.02 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 58: Fractional free volume 0.194 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (89 ms) 58: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: cutoff = 0.18 nm 58: probe_radius = 0 nm 58: seed = 17 58: ninsert = 1000 probes per nm^3 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 58: van der Spoel and Luciano T. Costa 58: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 58: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 58: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Free volume 38.48 +/- 0.00 % 58: Total volume 68.92 +/- 0.00 nm^3 58: Number of molecules 340 total mass 63491.38 Dalton 58: Average molar mass: 186.74 Dalton 58: Density rho: 1529.71 +/- 0.00 nm^3 58: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 58: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 58: Fractional free volume 0.200 +/- 0.000 58: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (96 ms) 58: [----------] 2 tests from FreeVolumeModuleTest (186 ms total) 58: 58: [----------] 11 tests from MsdModuleTest 58: [ RUN ] MsdModuleTest.threeDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.threeDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.twoDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.twoDimensionalDiffusion (1 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusion 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusion (5 ms) 58: [ RUN ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau 58: Reading frame 0 time 0.000 Reading frame 1 time 1.000 Reading frame 2 time 2.000 Reading frame 3 time 3.000 Reading frame 4 time 4.000 Reading frame 5 time 5.000 Reading frame 6 time 6.000 Reading frame 7 time 7.000 Reading frame 8 time 8.000 Reading frame 9 time 9.000 Last frame 9 time 9.000 58: Analyzed 10 frames, last time 9.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.oneDimensionalDiffusionWithMaxTau (1 ms) 58: [ RUN ] MsdModuleTest.roundingFail 58: Reading frame 0 time 0.000 Reading frame 1 time 0.001 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] MsdModuleTest.roundingFail (0 ms) 58: [ RUN ] MsdModuleTest.multipleGroupsWork 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_multipleGroupsWork.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -1251213377 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.multipleGroupsWork (32 ms) 58: [ DISABLED ] MsdModuleTest.DISABLED_trestartLessThanDt 58: [ RUN ] MsdModuleTest.trestartGreaterThanDt 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_trestartGreaterThanDt.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 1304255403 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.trestartGreaterThanDt (29 ms) 58: [ RUN ] MsdModuleTest.molTest 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_molTest.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to 2145869818 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.molTest (28 ms) 58: [ RUN ] MsdModuleTest.beginFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_beginFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -541016833 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.beginFit (30 ms) 58: [ RUN ] MsdModuleTest.endFit 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_endFit.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -751346001 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.endFit (26 ms) 58: [ RUN ] MsdModuleTest.notEnoughPointsForFitErrorEstimate 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file alanine_vsite_solvated.top, line 28]: 58: For energy conservation with LINCS, lincs_iter should be 2 or larger. 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 1818.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: NVE simulation: will use the initial temperature of 288.764 K for 58: determining the Verlet buffer size 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: There are 9 non-linear virtual site constructions. Their contribution to 58: the energy error is approximated. In most cases this does not affect the 58: error significantly. 58: 58: 58: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 5 NOTEs 58: NOTE: You provided an index file 58: /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/alanine_vsite_solvated.ndx 58: (with -n), but it was not used by any selection. 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/MsdModuleTest_notEnoughPointsForFitErrorEstimate.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 2.000 58: WARNING: -dt and -trestart are equal. Statistics for each tau data point will not be independent. 58: Reading frame 2 time 4.000 Reading frame 3 time 6.000 Reading frame 4 time 8.000 Reading frame 5 time 10.000 Reading frame 6 time 12.000 Reading frame 7 time 14.000 Reading frame 8 time 16.000 Reading frame 9 time 18.000 Reading frame 10 time 20.000 Reading frame 11 time 22.000 Reading frame 12 time 24.000 Reading frame 13 time 26.000 Reading frame 14 time 28.000 Reading frame 15 time 30.000 Reading frame 16 time 32.000 Reading frame 17 time 34.000 Reading frame 18 time 36.000 Reading frame 19 time 38.000 Reading frame 20 time 40.000 Last frame 20 time 40.000 58: Analyzed 21 frames, last time 40.000 58: Setting the LD random seed to -1376446465 58: 58: Generated 2145 of the 2145 non-bonded parameter combinations 58: 58: Generated 2145 of the 2145 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 58: 58: Excluding 2 bonded neighbours molecule type 'SOL' 58: 58: Cleaning up constraints and constant bonded interactions with virtual sites 58: 58: Converted 15 Bonds with virtual sites to connections, 7 left 58: 58: Removed 18 Angles with virtual sites, 21 left 58: 58: Removed 10 Proper Dih.s with virtual sites, 44 left 58: 58: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 288.764 K 58: 58: Calculated rlist for 1x1 atom pair-list as 0.910 nm, buffer size 0.060 nm 58: 58: Set rlist, assuming 4x4 atom pair-list, to 0.898 nm, buffer size 0.048 nm 58: 58: Note that mdrun will redetermine rlist based on the actual pair-list setup 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] MsdModuleTest.notEnoughPointsForFitErrorEstimate (30 ms) 58: [----------] 11 tests from MsdModuleTest (188 ms total) 58: 58: [----------] 9 tests from PairDistanceModuleTest 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistances (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (5 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (5 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (1 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (5 ms) 58: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (1 ms) 58: [----------] 9 tests from PairDistanceModuleTest (24 ms total) 58: 58: [----------] 5 tests from RdfModuleTest 58: [ RUN ] RdfModuleTest.BasicTest 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.BasicTest (19 ms) 58: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 58: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 58: Reading frame 0 time 0.000 Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (17 ms) 58: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (23 ms) 58: [ RUN ] RdfModuleTest.CalculatesSurf 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesSurf (13 ms) 58: [ RUN ] RdfModuleTest.CalculatesXY 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] RdfModuleTest.CalculatesXY (24 ms) 58: [----------] 5 tests from RdfModuleTest (98 ms total) 58: 58: [----------] 5 tests from SasaModuleTest 58: [ RUN ] SasaModuleTest.BasicTest 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.BasicTest (10 ms) 58: [ RUN ] SasaModuleTest.HandlesSelectedResidues 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesSelectedResidues (7 ms) 58: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (6 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (8 ms) 58: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 58: Michael Scharf 58: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 58: of Surface Area and Volume and to Dot Surface Contouring of Molecular 58: Assemblies 58: J. Comp. Chem. 16 (1995) pp. 273-284 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 58: from the source below. This means the results may be different 58: compared to previous GROMACS versions. 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. Bondi 58: van der Waals Volumes and Radii 58: J. Phys. Chem. 68 (1964) pp. 441-451 58: -------- -------- --- Thank You --- -------- -------- 58: 58: Analyzed topology coordinates 58: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (8 ms) 58: [----------] 5 tests from SasaModuleTest (41 ms total) 58: 58: [----------] 8 tests from SelectModuleTest 58: [ RUN ] SelectModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.BasicTest (7 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (5 ms) 58: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (1 ms) 58: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (4 ms) 58: [ RUN ] SelectModuleTest.NormalizesSizes 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.NormalizesSizes (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueNumbers 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueNumbers (1 ms) 58: [ RUN ] SelectModuleTest.WritesResidueIndices 58: Analyzed topology coordinates 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] SelectModuleTest.WritesResidueIndices (1 ms) 58: [----------] 8 tests from SelectModuleTest (25 ms total) 58: 58: [----------] 10 tests from SurfaceAreaTest 58: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 58: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 58: [ OK ] SurfaceAreaTest.ComputesTwoPoints (4 ms) 58: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 58: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints12 58: [ OK ] SurfaceAreaTest.SurfacePoints12 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints32 58: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints42 58: [ OK ] SurfaceAreaTest.SurfacePoints42 (0 ms) 58: [ RUN ] SurfaceAreaTest.SurfacePoints122 58: [ OK ] SurfaceAreaTest.SurfacePoints122 (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100Points 58: [ OK ] SurfaceAreaTest.Computes100Points (0 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (1 ms) 58: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 58: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (5 ms) 58: [----------] 10 tests from SurfaceAreaTest (13 ms total) 58: 58: [----------] 4 tests from TopologyInformation 58: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 58: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithGroFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithGroFile (1 ms) 58: [ RUN ] TopologyInformation.WorksWithPdbFile 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TopologyInformation.WorksWithPdbFile (0 ms) 58: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 58: 58: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: For a correct single-point energy evaluation with nsteps = 0, use 58: continuation = yes to avoid constraining the input coordinates. 58: 58: Generating 1-4 interactions: fudge = 0.5 58: 58: NOTE 2 [file lysozyme.top, line 1465]: 58: System has non-zero total charge: 2.000000 58: Total charge should normally be an integer. See 58: https://manual.gromacs.org/current/user-guide/floating-point.html 58: for discussion on how close it should be to an integer. 58: 58: 58: 58: Number of degrees of freedom in T-Coupling group rest is 465.00 58: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 58: 58: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: NVE simulation with an initial temperature of zero: will use a Verlet 58: buffer of 10%. Check your energy drift! 58: 58: 58: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 58: You are using a plain Coulomb cut-off, which might produce artifacts. 58: You might want to consider using PME electrostatics. 58: 58: 58: 58: There were 4 NOTEs 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 58: Setting the LD random seed to -1140916273 58: 58: Generated 330891 of the 330891 non-bonded parameter combinations 58: 58: Generated 330891 of the 330891 1-4 parameter combinations 58: 58: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 58: Analysing residue names: 58: There are: 10 Protein residues 58: Analysing Protein... 58: 58: This run will generate roughly 0 Mb of data 58: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (399 ms) 58: [----------] 4 tests from TopologyInformation (401 ms total) 58: 58: [----------] 4 tests from TrajectoryModuleTest 58: [ RUN ] TrajectoryModuleTest.BasicTest 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.BasicTest (2 ms) 58: [ RUN ] TrajectoryModuleTest.PlotsXOnly 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.PlotsXOnly (1 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (2 ms) 58: [ RUN ] TrajectoryModuleTest.HandlesNoForces 58: Reading frames from gro file 'Test system', 15 atoms. 58: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 58: Analyzed 2 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: [ OK ] TrajectoryModuleTest.HandlesNoForces (1 ms) 58: [----------] 4 tests from TrajectoryModuleTest (7 ms total) 58: 58: [----------] 5 tests from UnionFinderTest 58: [ RUN ] UnionFinderTest.WorksEmpty 58: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 58: [ RUN ] UnionFinderTest.BasicMerges 58: [ OK ] UnionFinderTest.BasicMerges (0 ms) 58: [ RUN ] UnionFinderTest.LargerMerges 58: [ OK ] UnionFinderTest.LargerMerges (0 ms) 58: [ RUN ] UnionFinderTest.LongRightMerge 58: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 58: [ RUN ] UnionFinderTest.LongLeftMerge 58: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 58: [----------] 5 tests from UnionFinderTest (0 ms total) 58: 58: [----------] 1 test from MappedUnionFinderTest 58: [ RUN ] MappedUnionFinderTest.BasicMerges 58: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 58: [----------] 1 test from MappedUnionFinderTest (0 ms total) 58: 58: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/0 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/0 (6 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/1 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/1 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/2 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/2 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/3 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/3 (6 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/4 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/4 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/5 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/5 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/6 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/6 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/7 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/7 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/8 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/8 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/9 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/9 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/10 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/10 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/11 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/11 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/12 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/12 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/13 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/13 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/14 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/14 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/15 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/15 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/16 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/16 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/17 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/17 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/18 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/18 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/19 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/19 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/20 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/20 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/21 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/21 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/22 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/22 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/23 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/23 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/24 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/24 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/25 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/25 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/26 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/26 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/27 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/27 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/28 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/28 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/29 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/29 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/30 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/30 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/31 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/31 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/32 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/32 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/33 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/33 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/34 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/34 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/35 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/35 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/36 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/36 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/37 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/37 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/38 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/38 (4 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/39 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/39 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/40 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/40 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/41 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/41 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/42 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/42 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/43 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/43 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/44 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/44 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/45 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/45 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/46 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/46 (8 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/47 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/47 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/48 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/48 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/49 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/49 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/50 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/50 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/51 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/51 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/52 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/52 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/53 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/53 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/54 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/54 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/55 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/55 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/56 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/56 (44 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/57 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/57 (40 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/58 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/58 (36 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/59 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/59 (36 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/60 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/60 (42 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/61 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/61 (42 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/62 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/62 (46 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/63 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/63 (42 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/64 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/64 (38 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/65 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/65 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/66 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/66 (37 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/67 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/67 (37 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/68 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/68 (36 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/69 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/69 (35 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/70 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/70 (39 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/71 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/71 (43 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/72 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/72 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/73 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/73 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/74 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/74 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/75 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/75 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/76 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/76 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/77 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/77 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/78 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/78 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/79 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/79 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/80 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/80 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/81 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/81 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/82 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/82 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/83 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/83 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/84 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/84 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/85 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/85 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/86 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/86 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/87 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/87 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/88 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/88 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/89 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/89 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/90 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/90 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/91 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/91 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/92 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/92 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/93 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/93 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/94 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/94 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/95 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/95 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/96 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/96 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/97 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/97 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/98 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/98 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/99 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/99 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/100 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/100 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/101 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/101 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/102 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/102 (36 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/103 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/103 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/104 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/104 (39 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/105 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/105 (35 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/106 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/106 (55 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/107 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/107 (31 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/108 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/108 (43 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/109 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/109 (51 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/110 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/110 (43 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/111 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/111 (35 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/112 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/112 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/113 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/113 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/114 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/114 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/115 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/115 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/116 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/116 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/117 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/117 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/118 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/118 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/119 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/119 (15 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/120 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/120 (85 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/121 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/121 (81 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/122 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/122 (106 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/123 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/123 (135 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/124 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/124 (161 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/125 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/125 (136 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/126 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/126 (107 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/127 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/127 (56 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/128 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/128 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/129 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/129 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/130 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/130 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/131 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/131 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/132 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/132 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/133 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/133 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/134 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/134 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/135 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/135 (9 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/136 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/136 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/137 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/137 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/138 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/138 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/139 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/139 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/140 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/140 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/141 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/141 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/142 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/142 (21 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/143 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/143 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/144 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/144 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/145 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/145 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/146 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/146 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/147 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/147 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/148 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/148 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/149 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/149 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/150 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/150 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/151 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/151 (10 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/152 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/152 (32 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/153 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/153 (36 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/154 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/154 (43 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/155 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/155 (47 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/156 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/156 (52 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/157 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/157 (52 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/158 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/158 (72 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNB.Works/159 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNB.Works/159 (64 ms) 58: [----------] 160 tests from MoleculeTests/DsspModuleTestDsspNB (3910 ms total) 58: 58: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/0 (96 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/1 (109 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/2 (82 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/3 (64 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/4 (65 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/5 (77 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/6 (61 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/7 (70 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/8 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/9 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/10 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/11 (22 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/12 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/13 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/14 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/15 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/16 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/17 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/18 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/19 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/20 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/21 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/22 (36 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNB.Works/23 (40 ms) 58: [----------] 24 tests from MoleculeTests/DsspModuleTestGromacsNB (1017 ms total) 58: 58: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/0 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/1 (29 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/2 (5 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 708 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/3 (25 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/4 (45 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/5 (37 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/6 (45 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2066 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/7 (37 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/8 (48 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/9 (48 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/10 (48 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2564 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/11 (48 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/12 (85 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/13 (118 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/14 (89 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 4666 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/15 (73 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/16 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/17 (17 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/18 (28 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 798 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/19 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/20 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/21 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/22 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1216 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/23 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/24 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/25 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/26 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1022 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/27 (19 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/28 (50 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/29 (53 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/30 (50 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 3419 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/31 (96 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/32 (71 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/33 (75 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/34 (39 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2923 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/35 (43 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/36 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/37 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/38 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1766 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/39 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/40 (65 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/41 (66 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/42 (33 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2745 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/43 (37 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/44 (23 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/45 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/46 (14 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1742 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/47 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/48 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/49 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/50 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1643 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/51 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/52 (13 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/53 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/54 (11 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1380 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/55 (12 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/56 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/57 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/58 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1060 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/59 (7 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/60 (64 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/61 (81 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/62 (83 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 5347 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/63 (114 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/64 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/65 (45 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/66 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1264 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/67 (20 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/68 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/69 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/70 (34 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1429 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/71 (30 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/72 (18 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/73 (42 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/74 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 1285 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/75 (26 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/76 (44 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/77 (40 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/78 (56 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 58: WARNING: all CONECT records are ignored 58: Reading frames from pdb fileWARNING: all CONECT records are ignored 58: Reading frame 0 time 0.000 '', 2595 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestDsspNoNB.Works/79 (48 ms) 58: [----------] 80 tests from MoleculeTests/DsspModuleTestDsspNoNB (2884 ms total) 58: 58: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/0 (105 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/1 (117 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/2 (83 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 5969 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/3 (81 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/4 (43 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/5 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/6 (35 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 1860 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/7 (27 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/8 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/9 (16 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/10 (24 ms) 58: [ RUN ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 58: Reading frames from pdb file Reading frame 0 time 500.000 '', 1422 atoms 58: Last frame 0 time 500.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: W. Kabsch, C. Sander 58: Dictionary of protein secondary structure: pattern recognition of 58: hydrogen-bonded and geometrical features. 58: Biopolymers 22 (1983) pp. 2577-2637 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: S. Gorelov, A. Titov, O. Tolicheva, A. Konevega, A. Shvetsov 58: DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in 58: Trajectories 58: Journal of Chemical Information and Modeling 0 (2024) pp. 0 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/DsspModuleTestGromacsNoNB.Works/11 (36 ms) 58: [----------] 12 tests from MoleculeTests/DsspModuleTestGromacsNoNB (624 ms total) 58: 58: [----------] 3 tests from GyrateTests/GyrateModuleTest 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/0 (8 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/1 (17 ms) 58: [ RUN ] GyrateTests/GyrateModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: [ OK ] GyrateTests/GyrateModuleTest.Works/2 (4 ms) 58: [----------] 3 tests from GyrateTests/GyrateModuleTest (31 ms total) 58: 58: [----------] 6 tests from HBondTests/HbondModuleTest 58: [ RUN ] HBondTests/HbondModuleTest.Works/0 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/0 (18 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/1 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Protein (304 atoms) and Protein (304 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/1 (23 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/2 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/2 (87 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/3 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Protein (304 atoms) and Water (3480 atoms) 58: Merging hbonds with Acceptor and Donor swapped 58: [ OK ] HBondTests/HbondModuleTest.Works/3 (80 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/4 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/4 (74 ms) 58: [ RUN ] HBondTests/HbondModuleTest.Works/5 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/trpcage.tpr, VERSION 2023-rc1 (single precision) 58: Reading frame 0 time 0.000 Reading frame 1 time 10.000 Last frame 1 time 10.000 58: Analyzed 2 frames, last time 10.000 58: Checking for overlap in atoms between Water (3480 atoms) and Water (3480 atoms) 58: [ OK ] HBondTests/HbondModuleTest.Works/5 (78 ms) 58: [----------] 6 tests from HBondTests/HbondModuleTest (404 ms total) 58: 58: [----------] 4 tests from MoleculeTests/ScatteringModule 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/0 (6 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.DirectMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer & J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A 24 (1968) pp. 321 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.DirectMode/1 (236 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/0 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/0 (17 ms) 58: [ RUN ] MoleculeTests/ScatteringModule.MCMode/1 58: Reading frames from pdb file Reading frame 0 time 0.000 '', 156 atoms 58: Last frame 0 time 0.000 58: Analyzed 1 frames, last time 0.000 58: 58: WARNING: Masses and atomic (Van der Waals) radii will be guessed 58: based on residue and atom names, since they could not be 58: definitively assigned from the information in your input 58: files. These guessed numbers might deviate from the mass 58: and radius of the atom type. Please check the output 58: files if necessary. Note, that this functionality may 58: be removed in a future GROMACS version. Please, consider 58: using another file format for your input. 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: A. V. Shvetsov, A. E. Schmidt, D. V. Lebedev & V. V. Isaev-Ivanov 58: Method for calculating small-angle neutron scattering spectra using all-atom 58: molecular dynamics trajectories 58: Journal of Surface Investigation. X-ray, Synchrotron and Neutron Techniques 7 (2013) pp. 1124–1127 58: -------- -------- --- Thank You --- -------- -------- 58: 58: 58: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 58: D. T. Cromer & J. B. Mann 58: X-ray scattering factors computed from numerical Hartree-Fock wave functions 58: Acta Cryst. A 24 (1968) pp. 321 58: -------- -------- --- Thank You --- -------- -------- 58: 58: [ OK ] MoleculeTests/ScatteringModule.MCMode/1 (102 ms) 58: [----------] 4 tests from MoleculeTests/ScatteringModule (364 ms total) 58: 58: [----------] Global test environment tear-down 58: [==========] 385 tests from 24 test suites ran. (10349 ms total) 58: [ PASSED ] 385 tests. 58: 58: YOU HAVE 1 DISABLED TEST 58: 58/91 Test #58: TrajectoryAnalysisUnitTests .................. Passed 10.56 sec test 59 Start 59: EnergyAnalysisUnitTests 59: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/energyanalysis-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/EnergyAnalysisUnitTests.xml" 59: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests 59: Test timeout computed to be: 30 59: [==========] Running 11 tests from 5 test suites. 59: [----------] Global test environment set-up. 59: [----------] 2 tests from EnergyTermTest 59: [ RUN ] EnergyTermTest.ConstructWorks 59: [ OK ] EnergyTermTest.ConstructWorks (0 ms) 59: [ RUN ] EnergyTermTest.AddFrameWorks 59: [ OK ] EnergyTermTest.AddFrameWorks (0 ms) 59: [----------] 2 tests from EnergyTermTest (0 ms total) 59: 59: [----------] 1 test from DhdlTest 59: [ RUN ] DhdlTest.ExtractDhdl 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 59: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 59: Note: file tpx version 110, software tpx version 134 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Reading energy frame 6 time 0.060 Reading energy frame 7 time 0.070 Reading energy frame 8 time 0.080 Reading energy frame 9 time 0.090 Reading energy frame 10 time 0.100 Reading energy frame 11 time 0.110 Reading energy frame 12 time 0.120 Reading energy frame 13 time 0.130 Reading energy frame 14 time 0.140 Reading energy frame 15 time 0.150 Reading energy frame 16 time 0.160 Reading energy frame 17 time 0.170 Reading energy frame 18 time 0.180 Reading energy frame 19 time 0.190 Reading energy frame 20 time 0.200 Reading energy frame 30 time 0.300 Reading energy frame 40 time 0.400 Reading energy frame 50 time 0.500 Reading energy frame 60 time 0.600 Reading energy frame 70 time 0.700 Reading energy frame 80 time 0.800 Reading energy frame 90 time 0.900 Reading energy frame 100 time 1.000 Last energy frame read 100 time 1.000 59: 59: 59: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 59: [ OK ] DhdlTest.ExtractDhdl (28 ms) 59: [----------] 1 test from DhdlTest (29 ms total) 59: 59: [----------] 1 test from OriresTest 59: [ RUN ] OriresTest.ExtractOrires 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 59: Reading file /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 59: Note: file tpx version 111, software tpx version 134 59: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 59: End your selection with 0 59: Selecting all 7 orientation restraints 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Reading energy frame 3 time 0.006 Reading energy frame 4 time 0.008 Reading energy frame 5 time 0.010 Reading energy frame 6 time 0.012 Reading energy frame 7 time 0.014 Reading energy frame 8 time 0.016 Reading energy frame 9 time 0.018 Reading energy frame 10 time 0.020 Last energy frame read 10 time 0.020 59: [ OK ] OriresTest.ExtractOrires (15 ms) 59: [----------] 1 test from OriresTest (15 ms total) 59: 59: [----------] 5 tests from EnergyTest 59: [ RUN ] EnergyTest.ExtractEnergy 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: [ OK ] EnergyTest.ExtractEnergy (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyByNumber 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 59: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 59: Pres. DC -268.49 3 8.52175 13.2804 (bar) 59: [ OK ] EnergyTest.ExtractEnergyByNumber (1 ms) 59: [ RUN ] EnergyTest.ExtractEnergyMixed 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 59: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 59: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 59: 13 Box-Z 14 Volume 15 Density 16 pV 59: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 59: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 59: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 59: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 59: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 59: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: [ OK ] EnergyTest.ExtractEnergyMixed (13 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInName 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 1 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInName (0 ms) 59: [ RUN ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener_numberInName.edr as single precision energy file 59: 59: Select the terms you want from the following list by 59: selecting either (part of) the name or the number or a combination. 59: End your selection with an empty line or a zero. 59: ------------------------------------------------------------------- 59: 1 Bond 2 Angle 3 Proper-Dih. 4 Per.-Imp.-Dih. 59: 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 59: 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 59: 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd 59: 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 59: 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 59: 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 59: 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 59: 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 2CosZ*Vel-X 59: 37 1/Viscosity 38 T-System 39 Lamb-System 59: 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Reading energy frame 2 time 0.004 Last energy frame read 2 time 0.004 59: 59: Statistics over 3 steps [ 0.0000 through 0.0040 ps ], 2 data sets 59: All statistics are over 3 points (frames) 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: LJ (SR) -14.1095 -- 0.384124 0.932214 (kJ/mol) 59: 1/Viscosity 57767.2 -- 10666.2 -25998 (m s/kg) 59: [ OK ] EnergyTest.ExtractEnergyWithNumberInNameAndAlsoByNumber (0 ms) 59: [----------] 5 tests from EnergyTest (17 ms total) 59: 59: [----------] 2 tests from ViscosityTest 59: [ RUN ] ViscosityTest.EinsteinViscosity 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosity (163 ms) 59: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 59: Opened /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 59: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.200 Reading energy frame 2 time 0.400 Reading energy frame 3 time 0.600 Reading energy frame 4 time 0.800 Reading energy frame 5 time 1.000 Reading energy frame 6 time 1.200 Reading energy frame 7 time 1.400 Reading energy frame 8 time 1.600 Reading energy frame 9 time 1.800 Reading energy frame 10 time 2.000 Reading energy frame 11 time 2.200 Reading energy frame 12 time 2.400 Reading energy frame 13 time 2.600 Reading energy frame 14 time 2.800 Reading energy frame 15 time 3.000 Reading energy frame 16 time 3.200 Reading energy frame 17 time 3.400 Reading energy frame 18 time 3.600 Reading energy frame 19 time 3.800 Reading energy frame 20 time 4.000 Reading energy frame 30 time 6.000 Reading energy frame 40 time 8.000 Reading energy frame 50 time 10.000 Last energy frame read 50 time 10.000 59: 59: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 59: All statistics are over 5001 points 59: 59: Energy Average Err.Est. RMSD Tot-Drift 59: ------------------------------------------------------------------------------- 59: Pres-XX 20.2092 65 717.193 185.978 (bar) 59: Pres-XY -47.7351 39 372.522 207.456 (bar) 59: Pres-XZ 11.477 31 379.79 6.80818 (bar) 59: Pres-YX -47.7106 39 372.525 207.5 (bar) 59: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 59: Pres-YZ -41.3534 45 401.216 114.663 (bar) 59: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 59: Pres-ZY -41.3119 45 401.196 114.743 (bar) 59: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 59: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 59: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 59: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 59: 59: Computing shear viscosity using the Einstein relation with 14 start points separated by 0.2 ps 59: [ OK ] ViscosityTest.EinsteinViscosityIntegral (71 ms) 59: [----------] 2 tests from ViscosityTest (235 ms total) 59: 59: [----------] Global test environment tear-down 59: [==========] 11 tests from 5 test suites ran. (298 ms total) 59: [ PASSED ] 11 tests. 59/91 Test #59: EnergyAnalysisUnitTests ...................... Passed 0.48 sec test 60 Start 60: ToolUnitTests 60: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/tool-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/ToolUnitTests.xml" 60: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests 60: Test timeout computed to be: 1920 60: [==========] Running 62 tests from 7 test suites. 60: [----------] Global test environment set-up. 60: [----------] 2 tests from DumpTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to -1082687666 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] DumpTest.WorksWithTpr 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr: 60: inputrec: 60: integrator = md 60: tinit = 0 60: dt = 0.001 60: nsteps = 0 60: init-step = 0 60: simulation-part = 1 60: mts = false 60: mass-repartition-factor = 1 60: comm-mode = Linear 60: nstcomm = 100 60: bd-fric = 0 60: ld-seed = -1082687666 60: emtol = 10 60: emstep = 0.01 60: niter = 20 60: fcstep = 0 60: nstcgsteep = 1000 60: nbfgscorr = 10 60: rtpi = 0.05 60: nstxout = 0 60: nstvout = 0 60: nstfout = 0 60: nstlog = 1000 60: nstcalcenergy = 100 60: nstenergy = 1000 60: nstxout-compressed = 0 60: compressed-x-precision = 1000 60: cutoff-scheme = Verlet 60: nstlist = 10 60: pbc = xyz 60: periodic-molecules = false 60: verlet-buffer-tolerance = -1 60: verlet-buffer-pressure-tolerance = 0.5 60: rlist = 1.1 60: coulombtype = Cut-off 60: coulomb-modifier = Potential-shift 60: rcoulomb-switch = 0 60: rcoulomb = 1 60: epsilon-r = 1 60: epsilon-rf = inf 60: vdw-type = Cut-off 60: vdw-modifier = Potential-shift 60: rvdw-switch = 0 60: rvdw = 1 60: DispCorr = No 60: table-extension = 1 60: fourierspacing = 0.12 60: fourier-nx = 0 60: fourier-ny = 0 60: fourier-nz = 0 60: pme-order = 4 60: ewald-rtol = 1e-05 60: ewald-rtol-lj = 0.001 60: lj-pme-comb-rule = Geometric 60: ewald-geometry = 3d 60: epsilon-surface = 0 60: ensemble-temperature-setting = not available 60: tcoupl = No 60: nsttcouple = -1 60: nh-chain-length = 0 60: print-nose-hoover-chain-variables = false 60: pcoupl = No 60: refcoord-scaling = No 60: posres-com (3): 60: posres-com[0]= 0.00000e+00 60: posres-com[1]= 0.00000e+00 60: posres-com[2]= 0.00000e+00 60: posres-comB (3): 60: posres-comB[0]= 0.00000e+00 60: posres-comB[1]= 0.00000e+00 60: posres-comB[2]= 0.00000e+00 60: QMMM = false 60: qm-opts: 60: ngQM = 0 60: constraint-algorithm = Lincs 60: continuation = false 60: Shake-SOR = false 60: shake-tol = 0.0001 60: lincs-order = 4 60: lincs-iter = 1 60: lincs-warnangle = 30 60: nwall = 0 60: wall-type = 9-3 60: wall-r-linpot = -1 60: wall-atomtype[0] = -1 60: wall-atomtype[1] = -1 60: wall-density[0] = 0 60: wall-density[1] = 0 60: wall-ewald-zfac = 3 60: pull = false 60: awh = false 60: rotation = false 60: interactiveMD = false 60: disre = No 60: disre-weighting = Conservative 60: disre-mixed = false 60: dr-fc = 1000 60: dr-tau = 0 60: nstdisreout = 100 60: orire-fc = 0 60: orire-tau = 0 60: nstorireout = 100 60: free-energy = no 60: cos-acceleration = 0 60: deform (3x3): 60: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: simulated-tempering = false 60: swapcoords = no 60: userint1 = 0 60: userint2 = 0 60: userint3 = 0 60: userint4 = 0 60: userreal1 = 0 60: userreal2 = 0 60: userreal3 = 0 60: userreal4 = 0 60: applied-forces: 60: electric-field: 60: x: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: y: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: z: 60: E0 = 0 60: omega = 0 60: t0 = 0 60: sigma = 0 60: density-guided-simulation: 60: active = false 60: group = protein 60: similarity-measure = inner-product 60: atom-spreading-weight = unity 60: force-constant = 1e+09 60: gaussian-transform-spreading-width = 0.2 60: gaussian-transform-spreading-range-in-multiples-of-width = 4 60: reference-density-filename = reference.mrc 60: nst = 1 60: normalize-densities = true 60: adaptive-force-scaling = false 60: adaptive-force-scaling-time-constant = 4 60: shift-vector = 60: transformation-matrix = 60: qmmm-cp2k: 60: active = false 60: qmgroup = System 60: qmmethod = PBE 60: qmfilenames = 60: qmcharge = 0 60: qmmultiplicity = 1 60: colvars: 60: active = false 60: configfile = 60: seed = -1 60: grpopts: 60: nrdf: 465 60: ref-t: 0 60: tau-t: 0 60: annealing: No 60: annealing-npoints: 0 60: acc: 0 0 0 60: nfreeze: N N N 60: energygrp-flags[ 0]: 0 60: header: 60: bIr = present 60: bBox = present 60: bTop = present 60: bX = present 60: bV = present 60: bF = not present 60: natoms = 156 60: lambda = 0.000000e+00 60: buffer size = 46180 60: topology: 60: name="First 10 residues from 1AKI" 60: #atoms = 156 60: #molblock = 1 60: molblock (0): 60: moltype = 0 "Protein_chain_B" 60: #molecules = 1 60: #posres_xA = 0 60: #posres_xB = 0 60: bIntermolecularInteractions = false 60: ffparams: 60: atnr=10 60: ntypes=212 60: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06 60: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 60: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 60: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 60: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 60: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 60: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 60: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 60: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 60: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06 60: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06 60: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 60: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 60: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 60: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 60: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 60: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 60: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 60: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07 60: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07 60: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08 60: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 60: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 60: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 60: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 60: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 60: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 60: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06 60: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06 60: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07 60: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05 60: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 60: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 60: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 60: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 60: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 60: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06 60: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06 60: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07 60: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06 60: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06 60: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 60: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 60: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 60: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 60: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06 60: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06 60: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07 60: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06 60: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06 60: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06 60: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 60: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 60: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 60: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07 60: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07 60: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08 60: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07 60: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07 60: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07 60: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08 60: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 60: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 60: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07 60: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07 60: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08 60: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07 60: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07 60: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07 60: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08 60: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08 60: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 60: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05 60: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00 60: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05 60: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06 60: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05 60: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06 60: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05 60: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07 60: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07 60: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05 60: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05 60: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05 60: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05 60: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05 60: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05 60: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05 60: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05 60: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05 60: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05 60: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05 60: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05 60: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05 60: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05 60: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05 60: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05 60: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05 60: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02 60: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02 60: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02 60: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02 60: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02 60: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02 60: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02 60: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02 60: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02 60: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02 60: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02 60: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02 60: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02 60: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02 60: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02 60: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02 60: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02 60: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02 60: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02 60: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02 60: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02 60: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02 60: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02 60: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02 60: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2 60: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2 60: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2 60: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00 60: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00 60: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07 60: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06 60: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06 60: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06 60: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00 60: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07 60: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06 60: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08 60: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07 60: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06 60: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07 60: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06 60: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06 60: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06 60: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06 60: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07 60: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07 60: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07 60: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06 60: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06 60: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08 60: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07 60: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08 60: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06 60: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07 60: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05 60: reppow = 12 60: fudgeQQ = 0.5 60: cmap 60: moltype (0): 60: name="Protein_chain_B" 60: atoms: 60: atom (156): 60: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6} 60: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6} 60: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6} 60: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1} 60: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7} 60: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1} 60: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6} 60: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8} 60: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7} 60: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1} 60: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6} 60: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6} 60: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6} 60: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1} 60: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6} 60: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8} 60: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7} 60: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1} 60: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6} 60: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6} 60: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1} 60: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6} 60: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1} 60: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6} 60: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8} 60: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7} 60: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1} 60: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6} 60: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1} 60: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6} 60: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8} 60: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1} 60: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6} 60: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6} 60: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6} 60: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1} 60: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1} 60: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6} 60: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7} 60: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1} 60: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6} 60: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8} 60: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7} 60: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1} 60: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6} 60: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6} 60: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1} 60: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16} 60: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1} 60: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6} 60: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8} 60: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7} 60: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1} 60: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6} 60: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6} 60: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1} 60: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6} 60: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8} 60: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7} 60: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1} 60: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6} 60: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6} 60: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6} 60: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6} 60: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1} 60: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6} 60: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8} 60: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7} 60: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1} 60: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6} 60: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6} 60: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1} 60: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6} 60: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8} 60: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7} 60: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1} 60: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6} 60: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6} 60: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1} 60: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6} 60: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8} 60: atom (156): 60: atom[0]={name="N"} 60: atom[1]={name="H1"} 60: atom[2]={name="H2"} 60: atom[3]={name="H3"} 60: atom[4]={name="CA"} 60: atom[5]={name="HA"} 60: atom[6]={name="CB"} 60: atom[7]={name="HB1"} 60: atom[8]={name="HB2"} 60: atom[9]={name="CG"} 60: atom[10]={name="HG1"} 60: atom[11]={name="HG2"} 60: atom[12]={name="CD"} 60: atom[13]={name="HD1"} 60: atom[14]={name="HD2"} 60: atom[15]={name="CE"} 60: atom[16]={name="HE1"} 60: atom[17]={name="HE2"} 60: atom[18]={name="NZ"} 60: atom[19]={name="HZ1"} 60: atom[20]={name="HZ2"} 60: atom[21]={name="HZ3"} 60: atom[22]={name="C"} 60: atom[23]={name="O"} 60: atom[24]={name="N"} 60: atom[25]={name="H"} 60: atom[26]={name="CA"} 60: atom[27]={name="HA"} 60: atom[28]={name="CB"} 60: atom[29]={name="HB"} 60: atom[30]={name="CG1"} 60: atom[31]={name="HG11"} 60: atom[32]={name="HG12"} 60: atom[33]={name="HG13"} 60: atom[34]={name="CG2"} 60: atom[35]={name="HG21"} 60: atom[36]={name="HG22"} 60: atom[37]={name="HG23"} 60: atom[38]={name="C"} 60: atom[39]={name="O"} 60: atom[40]={name="N"} 60: atom[41]={name="H"} 60: atom[42]={name="CA"} 60: atom[43]={name="HA"} 60: atom[44]={name="CB"} 60: atom[45]={name="HB1"} 60: atom[46]={name="HB2"} 60: atom[47]={name="CG"} 60: atom[48]={name="CD1"} 60: atom[49]={name="HD1"} 60: atom[50]={name="CD2"} 60: atom[51]={name="HD2"} 60: atom[52]={name="CE1"} 60: atom[53]={name="HE1"} 60: atom[54]={name="CE2"} 60: atom[55]={name="HE2"} 60: atom[56]={name="CZ"} 60: atom[57]={name="HZ"} 60: atom[58]={name="C"} 60: atom[59]={name="O"} 60: atom[60]={name="N"} 60: atom[61]={name="H"} 60: atom[62]={name="CA"} 60: atom[63]={name="HA1"} 60: atom[64]={name="HA2"} 60: atom[65]={name="C"} 60: atom[66]={name="O"} 60: atom[67]={name="N"} 60: atom[68]={name="H"} 60: atom[69]={name="CA"} 60: atom[70]={name="HA"} 60: atom[71]={name="CB"} 60: atom[72]={name="HB1"} 60: atom[73]={name="HB2"} 60: atom[74]={name="CG"} 60: atom[75]={name="HG1"} 60: atom[76]={name="HG2"} 60: atom[77]={name="CD"} 60: atom[78]={name="HD1"} 60: atom[79]={name="HD2"} 60: atom[80]={name="NE"} 60: atom[81]={name="HE"} 60: atom[82]={name="CZ"} 60: atom[83]={name="NH1"} 60: atom[84]={name="HH11"} 60: atom[85]={name="HH12"} 60: atom[86]={name="NH2"} 60: atom[87]={name="HH21"} 60: atom[88]={name="HH22"} 60: atom[89]={name="C"} 60: atom[90]={name="O"} 60: atom[91]={name="N"} 60: atom[92]={name="H"} 60: atom[93]={name="CA"} 60: atom[94]={name="HA"} 60: atom[95]={name="CB"} 60: atom[96]={name="HB1"} 60: atom[97]={name="HB2"} 60: atom[98]={name="SG"} 60: atom[99]={name="HG"} 60: atom[100]={name="C"} 60: atom[101]={name="O"} 60: atom[102]={name="N"} 60: atom[103]={name="H"} 60: atom[104]={name="CA"} 60: atom[105]={name="HA"} 60: atom[106]={name="CB"} 60: atom[107]={name="HB1"} 60: atom[108]={name="HB2"} 60: atom[109]={name="CG"} 60: atom[110]={name="HG1"} 60: atom[111]={name="HG2"} 60: atom[112]={name="CD"} 60: atom[113]={name="OE1"} 60: atom[114]={name="OE2"} 60: atom[115]={name="C"} 60: atom[116]={name="O"} 60: atom[117]={name="N"} 60: atom[118]={name="H"} 60: atom[119]={name="CA"} 60: atom[120]={name="HA"} 60: atom[121]={name="CB"} 60: atom[122]={name="HB1"} 60: atom[123]={name="HB2"} 60: atom[124]={name="CG"} 60: atom[125]={name="HG"} 60: atom[126]={name="CD1"} 60: atom[127]={name="HD11"} 60: atom[128]={name="HD12"} 60: atom[129]={name="HD13"} 60: atom[130]={name="CD2"} 60: atom[131]={name="HD21"} 60: atom[132]={name="HD22"} 60: atom[133]={name="HD23"} 60: atom[134]={name="C"} 60: atom[135]={name="O"} 60: atom[136]={name="N"} 60: atom[137]={name="H"} 60: atom[138]={name="CA"} 60: atom[139]={name="HA"} 60: atom[140]={name="CB"} 60: atom[141]={name="HB1"} 60: atom[142]={name="HB2"} 60: atom[143]={name="HB3"} 60: atom[144]={name="C"} 60: atom[145]={name="O"} 60: atom[146]={name="N"} 60: atom[147]={name="H"} 60: atom[148]={name="CA"} 60: atom[149]={name="HA"} 60: atom[150]={name="CB"} 60: atom[151]={name="HB1"} 60: atom[152]={name="HB2"} 60: atom[153]={name="HB3"} 60: atom[154]={name="C"} 60: atom[155]={name="O"} 60: type (156): 60: type[0]={name="opls_287",nameB="opls_287"} 60: type[1]={name="opls_290",nameB="opls_290"} 60: type[2]={name="opls_290",nameB="opls_290"} 60: type[3]={name="opls_290",nameB="opls_290"} 60: type[4]={name="opls_293B",nameB="opls_293B"} 60: type[5]={name="opls_140",nameB="opls_140"} 60: type[6]={name="opls_136",nameB="opls_136"} 60: type[7]={name="opls_140",nameB="opls_140"} 60: type[8]={name="opls_140",nameB="opls_140"} 60: type[9]={name="opls_136",nameB="opls_136"} 60: type[10]={name="opls_140",nameB="opls_140"} 60: type[11]={name="opls_140",nameB="opls_140"} 60: type[12]={name="opls_136",nameB="opls_136"} 60: type[13]={name="opls_140",nameB="opls_140"} 60: type[14]={name="opls_140",nameB="opls_140"} 60: type[15]={name="opls_292",nameB="opls_292"} 60: type[16]={name="opls_140",nameB="opls_140"} 60: type[17]={name="opls_140",nameB="opls_140"} 60: type[18]={name="opls_287",nameB="opls_287"} 60: type[19]={name="opls_290",nameB="opls_290"} 60: type[20]={name="opls_290",nameB="opls_290"} 60: type[21]={name="opls_290",nameB="opls_290"} 60: type[22]={name="opls_235",nameB="opls_235"} 60: type[23]={name="opls_236",nameB="opls_236"} 60: type[24]={name="opls_238",nameB="opls_238"} 60: type[25]={name="opls_241",nameB="opls_241"} 60: type[26]={name="opls_224B",nameB="opls_224B"} 60: type[27]={name="opls_140",nameB="opls_140"} 60: type[28]={name="opls_137",nameB="opls_137"} 60: type[29]={name="opls_140",nameB="opls_140"} 60: type[30]={name="opls_135",nameB="opls_135"} 60: type[31]={name="opls_140",nameB="opls_140"} 60: type[32]={name="opls_140",nameB="opls_140"} 60: type[33]={name="opls_140",nameB="opls_140"} 60: type[34]={name="opls_135",nameB="opls_135"} 60: type[35]={name="opls_140",nameB="opls_140"} 60: type[36]={name="opls_140",nameB="opls_140"} 60: type[37]={name="opls_140",nameB="opls_140"} 60: type[38]={name="opls_235",nameB="opls_235"} 60: type[39]={name="opls_236",nameB="opls_236"} 60: type[40]={name="opls_238",nameB="opls_238"} 60: type[41]={name="opls_241",nameB="opls_241"} 60: type[42]={name="opls_224B",nameB="opls_224B"} 60: type[43]={name="opls_140",nameB="opls_140"} 60: type[44]={name="opls_149",nameB="opls_149"} 60: type[45]={name="opls_140",nameB="opls_140"} 60: type[46]={name="opls_140",nameB="opls_140"} 60: type[47]={name="opls_145",nameB="opls_145"} 60: type[48]={name="opls_145",nameB="opls_145"} 60: type[49]={name="opls_146",nameB="opls_146"} 60: type[50]={name="opls_145",nameB="opls_145"} 60: type[51]={name="opls_146",nameB="opls_146"} 60: type[52]={name="opls_145",nameB="opls_145"} 60: type[53]={name="opls_146",nameB="opls_146"} 60: type[54]={name="opls_145",nameB="opls_145"} 60: type[55]={name="opls_146",nameB="opls_146"} 60: type[56]={name="opls_145",nameB="opls_145"} 60: type[57]={name="opls_146",nameB="opls_146"} 60: type[58]={name="opls_235",nameB="opls_235"} 60: type[59]={name="opls_236",nameB="opls_236"} 60: type[60]={name="opls_238",nameB="opls_238"} 60: type[61]={name="opls_241",nameB="opls_241"} 60: type[62]={name="opls_223B",nameB="opls_223B"} 60: type[63]={name="opls_140",nameB="opls_140"} 60: type[64]={name="opls_140",nameB="opls_140"} 60: type[65]={name="opls_235",nameB="opls_235"} 60: type[66]={name="opls_236",nameB="opls_236"} 60: type[67]={name="opls_238",nameB="opls_238"} 60: type[68]={name="opls_241",nameB="opls_241"} 60: type[69]={name="opls_224B",nameB="opls_224B"} 60: type[70]={name="opls_140",nameB="opls_140"} 60: type[71]={name="opls_136",nameB="opls_136"} 60: type[72]={name="opls_140",nameB="opls_140"} 60: type[73]={name="opls_140",nameB="opls_140"} 60: type[74]={name="opls_308",nameB="opls_308"} 60: type[75]={name="opls_140",nameB="opls_140"} 60: type[76]={name="opls_140",nameB="opls_140"} 60: type[77]={name="opls_307",nameB="opls_307"} 60: type[78]={name="opls_140",nameB="opls_140"} 60: type[79]={name="opls_140",nameB="opls_140"} 60: type[80]={name="opls_303",nameB="opls_303"} 60: type[81]={name="opls_304",nameB="opls_304"} 60: type[82]={name="opls_302",nameB="opls_302"} 60: type[83]={name="opls_300",nameB="opls_300"} 60: type[84]={name="opls_301",nameB="opls_301"} 60: type[85]={name="opls_301",nameB="opls_301"} 60: type[86]={name="opls_300",nameB="opls_300"} 60: type[87]={name="opls_301",nameB="opls_301"} 60: type[88]={name="opls_301",nameB="opls_301"} 60: type[89]={name="opls_235",nameB="opls_235"} 60: type[90]={name="opls_236",nameB="opls_236"} 60: type[91]={name="opls_238",nameB="opls_238"} 60: type[92]={name="opls_241",nameB="opls_241"} 60: type[93]={name="opls_224B",nameB="opls_224B"} 60: type[94]={name="opls_140",nameB="opls_140"} 60: type[95]={name="opls_206",nameB="opls_206"} 60: type[96]={name="opls_140",nameB="opls_140"} 60: type[97]={name="opls_140",nameB="opls_140"} 60: type[98]={name="opls_200",nameB="opls_200"} 60: type[99]={name="opls_204",nameB="opls_204"} 60: type[100]={name="opls_235",nameB="opls_235"} 60: type[101]={name="opls_236",nameB="opls_236"} 60: type[102]={name="opls_238",nameB="opls_238"} 60: type[103]={name="opls_241",nameB="opls_241"} 60: type[104]={name="opls_224B",nameB="opls_224B"} 60: type[105]={name="opls_140",nameB="opls_140"} 60: type[106]={name="opls_136",nameB="opls_136"} 60: type[107]={name="opls_140",nameB="opls_140"} 60: type[108]={name="opls_140",nameB="opls_140"} 60: type[109]={name="opls_274",nameB="opls_274"} 60: type[110]={name="opls_140",nameB="opls_140"} 60: type[111]={name="opls_140",nameB="opls_140"} 60: type[112]={name="opls_271",nameB="opls_271"} 60: type[113]={name="opls_272",nameB="opls_272"} 60: type[114]={name="opls_272",nameB="opls_272"} 60: type[115]={name="opls_235",nameB="opls_235"} 60: type[116]={name="opls_236",nameB="opls_236"} 60: type[117]={name="opls_238",nameB="opls_238"} 60: type[118]={name="opls_241",nameB="opls_241"} 60: type[119]={name="opls_224B",nameB="opls_224B"} 60: type[120]={name="opls_140",nameB="opls_140"} 60: type[121]={name="opls_136",nameB="opls_136"} 60: type[122]={name="opls_140",nameB="opls_140"} 60: type[123]={name="opls_140",nameB="opls_140"} 60: type[124]={name="opls_137",nameB="opls_137"} 60: type[125]={name="opls_140",nameB="opls_140"} 60: type[126]={name="opls_135",nameB="opls_135"} 60: type[127]={name="opls_140",nameB="opls_140"} 60: type[128]={name="opls_140",nameB="opls_140"} 60: type[129]={name="opls_140",nameB="opls_140"} 60: type[130]={name="opls_135",nameB="opls_135"} 60: type[131]={name="opls_140",nameB="opls_140"} 60: type[132]={name="opls_140",nameB="opls_140"} 60: type[133]={name="opls_140",nameB="opls_140"} 60: type[134]={name="opls_235",nameB="opls_235"} 60: type[135]={name="opls_236",nameB="opls_236"} 60: type[136]={name="opls_238",nameB="opls_238"} 60: type[137]={name="opls_241",nameB="opls_241"} 60: type[138]={name="opls_224B",nameB="opls_224B"} 60: type[139]={name="opls_140",nameB="opls_140"} 60: type[140]={name="opls_135",nameB="opls_135"} 60: type[141]={name="opls_140",nameB="opls_140"} 60: type[142]={name="opls_140",nameB="opls_140"} 60: type[143]={name="opls_140",nameB="opls_140"} 60: type[144]={name="opls_235",nameB="opls_235"} 60: type[145]={name="opls_236",nameB="opls_236"} 60: type[146]={name="opls_238",nameB="opls_238"} 60: type[147]={name="opls_241",nameB="opls_241"} 60: type[148]={name="opls_224B",nameB="opls_224B"} 60: type[149]={name="opls_140",nameB="opls_140"} 60: type[150]={name="opls_135",nameB="opls_135"} 60: type[151]={name="opls_140",nameB="opls_140"} 60: type[152]={name="opls_140",nameB="opls_140"} 60: type[153]={name="opls_140",nameB="opls_140"} 60: type[154]={name="opls_235",nameB="opls_235"} 60: type[155]={name="opls_236",nameB="opls_236"} 60: residue (10): 60: residue[0]={name="LYS", nr=1, ic=' '} 60: residue[1]={name="VAL", nr=2, ic=' '} 60: residue[2]={name="PHE", nr=3, ic=' '} 60: residue[3]={name="GLY", nr=4, ic=' '} 60: residue[4]={name="ARG", nr=5, ic=' '} 60: residue[5]={name="CYS", nr=6, ic=' '} 60: residue[6]={name="GLU", nr=7, ic=' '} 60: residue[7]={name="LEU", nr=8, ic=' '} 60: residue[8]={name="ALA", nr=9, ic=' '} 60: residue[9]={name="ALA", nr=10, ic=' '} 60: excls: 60: numLists=156 60: numElements=1828 60: excls[0][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[1][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[2][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[3][num=8]={0, 1, 2, 3, 4, 5, 6, 22} 60: excls[4][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 60: 23, 24, 25, 26} 60: excls[5][num=13]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24} 60: excls[6][num=19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 60: 14, 15, 22, 23, 24} 60: excls[7][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[8][num=11]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22} 60: excls[9][num=17]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 60: 16, 17, 18, 22} 60: excls[10][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[11][num=11]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15} 60: excls[12][num=17]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 60: 17, 18, 19, 20, 21} 60: excls[13][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[14][num=11]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18} 60: excls[15][num=14]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 60: 20, 21} 60: excls[16][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[17][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[18][num=11]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21} 60: excls[19][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[20][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[21][num=8]={12, 15, 16, 17, 18, 19, 20, 21} 60: excls[22][num=18]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 60: 26, 27, 28, 38} 60: excls[23][num=9]={0, 4, 5, 6, 22, 23, 24, 25, 26} 60: excls[24][num=17]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 60: 30, 34, 38, 39, 40} 60: excls[25][num=9]={4, 22, 23, 24, 25, 26, 27, 28, 38} 60: excls[26][num=22]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 60: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42} 60: excls[27][num=12]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40} 60: excls[28][num=18]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 60: 34, 35, 36, 37, 38, 39, 40} 60: excls[29][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[30][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[31][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[32][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[33][num=8]={26, 28, 29, 30, 31, 32, 33, 34} 60: excls[34][num=14]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 60: 36, 37, 38} 60: excls[35][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[36][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[37][num=8]={26, 28, 29, 30, 34, 35, 36, 37} 60: excls[38][num=17]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39, 60: 40, 41, 42, 43, 44, 58} 60: excls[39][num=9]={24, 26, 27, 28, 38, 39, 40, 41, 42} 60: excls[40][num=17]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 60: 45, 46, 47, 58, 59, 60} 60: excls[41][num=9]={26, 38, 39, 40, 41, 42, 43, 44, 58} 60: excls[42][num=18]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 60: 48, 50, 58, 59, 60, 61, 62} 60: excls[43][num=12]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60} 60: excls[44][num=18]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 60: 50, 51, 52, 54, 58, 59, 60} 60: excls[45][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[46][num=10]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58} 60: excls[47][num=17]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 60: 52, 53, 54, 55, 56, 58} 60: excls[48][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 60: 54, 56, 57} 60: excls[49][num=8]={44, 47, 48, 49, 50, 52, 53, 56} 60: excls[50][num=14]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 60: 55, 56, 57} 60: excls[51][num=8]={44, 47, 48, 50, 51, 54, 55, 56} 60: excls[52][num=11]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57} 60: excls[53][num=8]={47, 48, 49, 52, 53, 54, 56, 57} 60: excls[54][num=11]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[55][num=8]={47, 50, 51, 52, 54, 55, 56, 57} 60: excls[56][num=11]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57} 60: excls[57][num=8]={48, 50, 52, 53, 54, 55, 56, 57} 60: excls[58][num=17]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60: 60, 61, 62, 63, 64, 65} 60: excls[59][num=9]={40, 42, 43, 44, 58, 59, 60, 61, 62} 60: excls[60][num=14]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64, 60: 65, 66, 67} 60: excls[61][num=9]={42, 58, 59, 60, 61, 62, 63, 64, 65} 60: excls[62][num=13]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 60: 68, 69} 60: excls[63][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[64][num=9]={58, 60, 61, 62, 63, 64, 65, 66, 67} 60: excls[65][num=14]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 60: 70, 71, 89} 60: excls[66][num=9]={60, 62, 63, 64, 65, 66, 67, 68, 69} 60: excls[67][num=17]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 60: 72, 73, 74, 89, 90, 91} 60: excls[68][num=9]={62, 65, 66, 67, 68, 69, 70, 71, 89} 60: excls[69][num=19]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 60: 75, 76, 77, 89, 90, 91, 92, 93} 60: excls[70][num=12]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91} 60: excls[71][num=18]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 60: 77, 78, 79, 80, 89, 90, 91} 60: excls[72][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[73][num=11]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89} 60: excls[74][num=16]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 60: 79, 80, 81, 82, 89} 60: excls[75][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[76][num=11]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80} 60: excls[77][num=15]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 60: 81, 82, 83, 86} 60: excls[78][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[79][num=10]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82} 60: excls[80][num=16]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 60: 84, 85, 86, 87, 88} 60: excls[81][num=9]={74, 77, 78, 79, 80, 81, 82, 83, 86} 60: excls[82][num=13]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 60: 87, 88} 60: excls[83][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[84][num=6]={80, 82, 83, 84, 85, 86} 60: excls[85][num=6]={80, 82, 83, 84, 85, 86} 60: excls[86][num=10]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88} 60: excls[87][num=6]={80, 82, 83, 86, 87, 88} 60: excls[88][num=6]={80, 82, 83, 86, 87, 88} 60: excls[89][num=17]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90, 60: 91, 92, 93, 94, 95, 100} 60: excls[90][num=9]={67, 69, 70, 71, 89, 90, 91, 92, 93} 60: excls[91][num=17]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94, 95, 60: 96, 97, 98, 100, 101, 102} 60: excls[92][num=9]={69, 89, 90, 91, 92, 93, 94, 95, 100} 60: excls[93][num=17]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 60: 99, 100, 101, 102, 103, 104} 60: excls[94][num=12]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102} 60: excls[95][num=13]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 60: 101, 102} 60: excls[96][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[97][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[98][num=9]={91, 93, 94, 95, 96, 97, 98, 99, 100} 60: excls[99][num=6]={93, 95, 96, 97, 98, 99} 60: excls[100][num=17]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100, 101, 60: 102, 103, 104, 105, 106, 115} 60: excls[101][num=9]={91, 93, 94, 95, 100, 101, 102, 103, 104} 60: excls[102][num=17]={91, 93, 94, 95, 100, 101, 102, 103, 104, 105, 60: 106, 107, 108, 109, 115, 116, 117} 60: excls[103][num=9]={93, 100, 101, 102, 103, 104, 105, 106, 115} 60: excls[104][num=19]={93, 100, 101, 102, 103, 104, 105, 106, 107, 60: 108, 109, 110, 111, 112, 115, 116, 117, 118, 119} 60: excls[105][num=12]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117} 60: excls[106][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 110, 111, 112, 113, 114, 115, 116, 117} 60: excls[107][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[108][num=11]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 115} 60: excls[109][num=13]={102, 104, 105, 106, 107, 108, 109, 110, 111, 60: 112, 113, 114, 115} 60: excls[110][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[111][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[112][num=10]={104, 106, 107, 108, 109, 110, 111, 112, 113, 60: 114} 60: excls[113][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[114][num=7]={106, 109, 110, 111, 112, 113, 114} 60: excls[115][num=17]={100, 102, 103, 104, 105, 106, 107, 108, 109, 60: 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[116][num=9]={102, 104, 105, 106, 115, 116, 117, 118, 119} 60: excls[117][num=17]={102, 104, 105, 106, 115, 116, 117, 118, 119, 60: 120, 121, 122, 123, 124, 134, 135, 136} 60: excls[118][num=9]={104, 115, 116, 117, 118, 119, 120, 121, 134} 60: excls[119][num=19]={104, 115, 116, 117, 118, 119, 120, 121, 122, 60: 123, 124, 125, 126, 130, 134, 135, 136, 137, 138} 60: excls[120][num=12]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136} 60: excls[121][num=21]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136} 60: excls[122][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[123][num=11]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 130, 134} 60: excls[124][num=17]={117, 119, 120, 121, 122, 123, 124, 125, 126, 60: 127, 128, 129, 130, 131, 132, 133, 134} 60: excls[125][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[126][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[127][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[128][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[129][num=8]={121, 124, 125, 126, 127, 128, 129, 130} 60: excls[130][num=14]={119, 121, 122, 123, 124, 125, 126, 127, 128, 60: 129, 130, 131, 132, 133} 60: excls[131][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[132][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[133][num=8]={121, 124, 125, 126, 130, 131, 132, 133} 60: excls[134][num=17]={115, 117, 118, 119, 120, 121, 122, 123, 124, 60: 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[135][num=9]={117, 119, 120, 121, 134, 135, 136, 137, 138} 60: excls[136][num=17]={117, 119, 120, 121, 134, 135, 136, 137, 138, 60: 139, 140, 141, 142, 143, 144, 145, 146} 60: excls[137][num=9]={119, 134, 135, 136, 137, 138, 139, 140, 144} 60: excls[138][num=16]={119, 134, 135, 136, 137, 138, 139, 140, 141, 60: 142, 143, 144, 145, 146, 147, 148} 60: excls[139][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[140][num=12]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146} 60: excls[141][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[142][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[143][num=8]={136, 138, 139, 140, 141, 142, 143, 144} 60: excls[144][num=17]={134, 136, 137, 138, 139, 140, 141, 142, 143, 60: 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[145][num=9]={136, 138, 139, 140, 144, 145, 146, 147, 148} 60: excls[146][num=16]={136, 138, 139, 140, 144, 145, 146, 147, 148, 60: 149, 150, 151, 152, 153, 154, 155} 60: excls[147][num=9]={138, 144, 145, 146, 147, 148, 149, 150, 154} 60: excls[148][num=13]={138, 144, 145, 146, 147, 148, 149, 150, 151, 60: 152, 153, 154, 155} 60: excls[149][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[150][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[151][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[152][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[153][num=8]={146, 148, 149, 150, 151, 152, 153, 154} 60: excls[154][num=11]={144, 146, 147, 148, 149, 150, 151, 152, 153, 60: 154, 155} 60: excls[155][num=6]={146, 148, 149, 150, 154, 155} 60: Bond: 60: nr: 468 60: iatoms: 60: 0 type=100 (BONDS) 0 1 60: 1 type=100 (BONDS) 0 2 60: 2 type=100 (BONDS) 0 3 60: 3 type=101 (BONDS) 0 4 60: 4 type=102 (BONDS) 4 5 60: 5 type=103 (BONDS) 4 6 60: 6 type=104 (BONDS) 4 22 60: 7 type=102 (BONDS) 6 7 60: 8 type=102 (BONDS) 6 8 60: 9 type=103 (BONDS) 6 9 60: 10 type=102 (BONDS) 9 10 60: 11 type=102 (BONDS) 9 11 60: 12 type=103 (BONDS) 9 12 60: 13 type=102 (BONDS) 12 13 60: 14 type=102 (BONDS) 12 14 60: 15 type=103 (BONDS) 12 15 60: 16 type=102 (BONDS) 15 16 60: 17 type=102 (BONDS) 15 17 60: 18 type=101 (BONDS) 15 18 60: 19 type=100 (BONDS) 18 19 60: 20 type=100 (BONDS) 18 20 60: 21 type=100 (BONDS) 18 21 60: 22 type=105 (BONDS) 22 23 60: 23 type=106 (BONDS) 22 24 60: 24 type=100 (BONDS) 24 25 60: 25 type=107 (BONDS) 24 26 60: 26 type=102 (BONDS) 26 27 60: 27 type=103 (BONDS) 26 28 60: 28 type=104 (BONDS) 26 38 60: 29 type=102 (BONDS) 28 29 60: 30 type=103 (BONDS) 28 30 60: 31 type=103 (BONDS) 28 34 60: 32 type=102 (BONDS) 30 31 60: 33 type=102 (BONDS) 30 32 60: 34 type=102 (BONDS) 30 33 60: 35 type=102 (BONDS) 34 35 60: 36 type=102 (BONDS) 34 36 60: 37 type=102 (BONDS) 34 37 60: 38 type=105 (BONDS) 38 39 60: 39 type=106 (BONDS) 38 40 60: 40 type=100 (BONDS) 40 41 60: 41 type=107 (BONDS) 40 42 60: 42 type=102 (BONDS) 42 43 60: 43 type=103 (BONDS) 42 44 60: 44 type=104 (BONDS) 42 58 60: 45 type=102 (BONDS) 44 45 60: 46 type=102 (BONDS) 44 46 60: 47 type=108 (BONDS) 44 47 60: 48 type=109 (BONDS) 47 48 60: 49 type=109 (BONDS) 47 50 60: 50 type=110 (BONDS) 48 49 60: 51 type=109 (BONDS) 48 52 60: 52 type=110 (BONDS) 50 51 60: 53 type=109 (BONDS) 50 54 60: 54 type=110 (BONDS) 52 53 60: 55 type=109 (BONDS) 52 56 60: 56 type=110 (BONDS) 54 55 60: 57 type=109 (BONDS) 54 56 60: 58 type=110 (BONDS) 56 57 60: 59 type=105 (BONDS) 58 59 60: 60 type=106 (BONDS) 58 60 60: 61 type=100 (BONDS) 60 61 60: 62 type=107 (BONDS) 60 62 60: 63 type=102 (BONDS) 62 63 60: 64 type=102 (BONDS) 62 64 60: 65 type=104 (BONDS) 62 65 60: 66 type=105 (BONDS) 65 66 60: 67 type=106 (BONDS) 65 67 60: 68 type=100 (BONDS) 67 68 60: 69 type=107 (BONDS) 67 69 60: 70 type=102 (BONDS) 69 70 60: 71 type=103 (BONDS) 69 71 60: 72 type=104 (BONDS) 69 89 60: 73 type=102 (BONDS) 71 72 60: 74 type=102 (BONDS) 71 73 60: 75 type=103 (BONDS) 71 74 60: 76 type=102 (BONDS) 74 75 60: 77 type=102 (BONDS) 74 76 60: 78 type=103 (BONDS) 74 77 60: 79 type=102 (BONDS) 77 78 60: 80 type=102 (BONDS) 77 79 60: 81 type=111 (BONDS) 77 80 60: 82 type=100 (BONDS) 80 81 60: 83 type=112 (BONDS) 80 82 60: 84 type=112 (BONDS) 82 83 60: 85 type=112 (BONDS) 82 86 60: 86 type=100 (BONDS) 83 84 60: 87 type=100 (BONDS) 83 85 60: 88 type=100 (BONDS) 86 87 60: 89 type=100 (BONDS) 86 88 60: 90 type=105 (BONDS) 89 90 60: 91 type=106 (BONDS) 89 91 60: 92 type=100 (BONDS) 91 92 60: 93 type=107 (BONDS) 91 93 60: 94 type=102 (BONDS) 93 94 60: 95 type=103 (BONDS) 93 95 60: 96 type=104 (BONDS) 93 100 60: 97 type=102 (BONDS) 95 96 60: 98 type=102 (BONDS) 95 97 60: 99 type=113 (BONDS) 95 98 60: 100 type=114 (BONDS) 98 99 60: 101 type=105 (BONDS) 100 101 60: 102 type=106 (BONDS) 100 102 60: 103 type=100 (BONDS) 102 103 60: 104 type=107 (BONDS) 102 104 60: 105 type=102 (BONDS) 104 105 60: 106 type=103 (BONDS) 104 106 60: 107 type=104 (BONDS) 104 115 60: 108 type=102 (BONDS) 106 107 60: 109 type=102 (BONDS) 106 108 60: 110 type=103 (BONDS) 106 109 60: 111 type=102 (BONDS) 109 110 60: 112 type=102 (BONDS) 109 111 60: 113 type=104 (BONDS) 109 112 60: 114 type=115 (BONDS) 112 113 60: 115 type=115 (BONDS) 112 114 60: 116 type=105 (BONDS) 115 116 60: 117 type=106 (BONDS) 115 117 60: 118 type=100 (BONDS) 117 118 60: 119 type=107 (BONDS) 117 119 60: 120 type=102 (BONDS) 119 120 60: 121 type=103 (BONDS) 119 121 60: 122 type=104 (BONDS) 119 134 60: 123 type=102 (BONDS) 121 122 60: 124 type=102 (BONDS) 121 123 60: 125 type=103 (BONDS) 121 124 60: 126 type=102 (BONDS) 124 125 60: 127 type=103 (BONDS) 124 126 60: 128 type=103 (BONDS) 124 130 60: 129 type=102 (BONDS) 126 127 60: 130 type=102 (BONDS) 126 128 60: 131 type=102 (BONDS) 126 129 60: 132 type=102 (BONDS) 130 131 60: 133 type=102 (BONDS) 130 132 60: 134 type=102 (BONDS) 130 133 60: 135 type=105 (BONDS) 134 135 60: 136 type=106 (BONDS) 134 136 60: 137 type=100 (BONDS) 136 137 60: 138 type=107 (BONDS) 136 138 60: 139 type=102 (BONDS) 138 139 60: 140 type=103 (BONDS) 138 140 60: 141 type=104 (BONDS) 138 144 60: 142 type=102 (BONDS) 140 141 60: 143 type=102 (BONDS) 140 142 60: 144 type=102 (BONDS) 140 143 60: 145 type=105 (BONDS) 144 145 60: 146 type=106 (BONDS) 144 146 60: 147 type=100 (BONDS) 146 147 60: 148 type=107 (BONDS) 146 148 60: 149 type=102 (BONDS) 148 149 60: 150 type=103 (BONDS) 148 150 60: 151 type=104 (BONDS) 148 154 60: 152 type=102 (BONDS) 150 151 60: 153 type=102 (BONDS) 150 152 60: 154 type=102 (BONDS) 150 153 60: 155 type=105 (BONDS) 154 155 60: G96Bond: 60: nr: 0 60: Morse: 60: nr: 0 60: Cubic Bonds: 60: nr: 0 60: Connect Bonds: 60: nr: 0 60: Harmonic Pot.: 60: nr: 0 60: FENE Bonds: 60: nr: 0 60: Tab. Bonds: 60: nr: 0 60: Tab. Bonds NC: 60: nr: 0 60: Restraint Pot.: 60: nr: 0 60: Angle: 60: nr: 1124 60: iatoms: 60: 0 type=116 (ANGLES) 1 0 2 60: 1 type=116 (ANGLES) 1 0 3 60: 2 type=116 (ANGLES) 1 0 4 60: 3 type=116 (ANGLES) 2 0 3 60: 4 type=116 (ANGLES) 2 0 4 60: 5 type=116 (ANGLES) 3 0 4 60: 6 type=116 (ANGLES) 0 4 5 60: 7 type=117 (ANGLES) 0 4 6 60: 8 type=117 (ANGLES) 0 4 22 60: 9 type=118 (ANGLES) 5 4 6 60: 10 type=116 (ANGLES) 5 4 22 60: 11 type=119 (ANGLES) 6 4 22 60: 12 type=118 (ANGLES) 4 6 7 60: 13 type=118 (ANGLES) 4 6 8 60: 14 type=120 (ANGLES) 4 6 9 60: 15 type=121 (ANGLES) 7 6 8 60: 16 type=118 (ANGLES) 7 6 9 60: 17 type=118 (ANGLES) 8 6 9 60: 18 type=118 (ANGLES) 6 9 10 60: 19 type=118 (ANGLES) 6 9 11 60: 20 type=120 (ANGLES) 6 9 12 60: 21 type=121 (ANGLES) 10 9 11 60: 22 type=118 (ANGLES) 10 9 12 60: 23 type=118 (ANGLES) 11 9 12 60: 24 type=118 (ANGLES) 9 12 13 60: 25 type=118 (ANGLES) 9 12 14 60: 26 type=120 (ANGLES) 9 12 15 60: 27 type=121 (ANGLES) 13 12 14 60: 28 type=118 (ANGLES) 13 12 15 60: 29 type=118 (ANGLES) 14 12 15 60: 30 type=118 (ANGLES) 12 15 16 60: 31 type=118 (ANGLES) 12 15 17 60: 32 type=117 (ANGLES) 12 15 18 60: 33 type=121 (ANGLES) 16 15 17 60: 34 type=116 (ANGLES) 16 15 18 60: 35 type=116 (ANGLES) 17 15 18 60: 36 type=116 (ANGLES) 15 18 19 60: 37 type=116 (ANGLES) 15 18 20 60: 38 type=116 (ANGLES) 15 18 21 60: 39 type=116 (ANGLES) 19 18 20 60: 40 type=116 (ANGLES) 19 18 21 60: 41 type=116 (ANGLES) 20 18 21 60: 42 type=122 (ANGLES) 4 22 23 60: 43 type=123 (ANGLES) 4 22 24 60: 44 type=124 (ANGLES) 23 22 24 60: 45 type=125 (ANGLES) 22 24 25 60: 46 type=126 (ANGLES) 22 24 26 60: 47 type=127 (ANGLES) 25 24 26 60: 48 type=116 (ANGLES) 24 26 27 60: 49 type=128 (ANGLES) 24 26 28 60: 50 type=129 (ANGLES) 24 26 38 60: 51 type=118 (ANGLES) 27 26 28 60: 52 type=116 (ANGLES) 27 26 38 60: 53 type=119 (ANGLES) 28 26 38 60: 54 type=118 (ANGLES) 26 28 29 60: 55 type=120 (ANGLES) 26 28 30 60: 56 type=120 (ANGLES) 26 28 34 60: 57 type=118 (ANGLES) 29 28 30 60: 58 type=118 (ANGLES) 29 28 34 60: 59 type=120 (ANGLES) 30 28 34 60: 60 type=118 (ANGLES) 28 30 31 60: 61 type=118 (ANGLES) 28 30 32 60: 62 type=118 (ANGLES) 28 30 33 60: 63 type=121 (ANGLES) 31 30 32 60: 64 type=121 (ANGLES) 31 30 33 60: 65 type=121 (ANGLES) 32 30 33 60: 66 type=118 (ANGLES) 28 34 35 60: 67 type=118 (ANGLES) 28 34 36 60: 68 type=118 (ANGLES) 28 34 37 60: 69 type=121 (ANGLES) 35 34 36 60: 70 type=121 (ANGLES) 35 34 37 60: 71 type=121 (ANGLES) 36 34 37 60: 72 type=122 (ANGLES) 26 38 39 60: 73 type=123 (ANGLES) 26 38 40 60: 74 type=124 (ANGLES) 39 38 40 60: 75 type=125 (ANGLES) 38 40 41 60: 76 type=126 (ANGLES) 38 40 42 60: 77 type=127 (ANGLES) 41 40 42 60: 78 type=116 (ANGLES) 40 42 43 60: 79 type=128 (ANGLES) 40 42 44 60: 80 type=129 (ANGLES) 40 42 58 60: 81 type=118 (ANGLES) 43 42 44 60: 82 type=116 (ANGLES) 43 42 58 60: 83 type=119 (ANGLES) 44 42 58 60: 84 type=118 (ANGLES) 42 44 45 60: 85 type=118 (ANGLES) 42 44 46 60: 86 type=130 (ANGLES) 42 44 47 60: 87 type=121 (ANGLES) 45 44 46 60: 88 type=116 (ANGLES) 45 44 47 60: 89 type=116 (ANGLES) 46 44 47 60: 90 type=131 (ANGLES) 44 47 48 60: 91 type=131 (ANGLES) 44 47 50 60: 92 type=132 (ANGLES) 48 47 50 60: 93 type=133 (ANGLES) 47 48 49 60: 94 type=132 (ANGLES) 47 48 52 60: 95 type=133 (ANGLES) 49 48 52 60: 96 type=133 (ANGLES) 47 50 51 60: 97 type=132 (ANGLES) 47 50 54 60: 98 type=133 (ANGLES) 51 50 54 60: 99 type=133 (ANGLES) 48 52 53 60: 100 type=132 (ANGLES) 48 52 56 60: 101 type=133 (ANGLES) 53 52 56 60: 102 type=133 (ANGLES) 50 54 55 60: 103 type=132 (ANGLES) 50 54 56 60: 104 type=133 (ANGLES) 55 54 56 60: 105 type=132 (ANGLES) 52 56 54 60: 106 type=133 (ANGLES) 52 56 57 60: 107 type=133 (ANGLES) 54 56 57 60: 108 type=122 (ANGLES) 42 58 59 60: 109 type=123 (ANGLES) 42 58 60 60: 110 type=124 (ANGLES) 59 58 60 60: 111 type=125 (ANGLES) 58 60 61 60: 112 type=126 (ANGLES) 58 60 62 60: 113 type=127 (ANGLES) 61 60 62 60: 114 type=116 (ANGLES) 60 62 63 60: 115 type=116 (ANGLES) 60 62 64 60: 116 type=129 (ANGLES) 60 62 65 60: 117 type=121 (ANGLES) 63 62 64 60: 118 type=116 (ANGLES) 63 62 65 60: 119 type=116 (ANGLES) 64 62 65 60: 120 type=122 (ANGLES) 62 65 66 60: 121 type=123 (ANGLES) 62 65 67 60: 122 type=124 (ANGLES) 66 65 67 60: 123 type=125 (ANGLES) 65 67 68 60: 124 type=126 (ANGLES) 65 67 69 60: 125 type=127 (ANGLES) 68 67 69 60: 126 type=116 (ANGLES) 67 69 70 60: 127 type=128 (ANGLES) 67 69 71 60: 128 type=129 (ANGLES) 67 69 89 60: 129 type=118 (ANGLES) 70 69 71 60: 130 type=116 (ANGLES) 70 69 89 60: 131 type=119 (ANGLES) 71 69 89 60: 132 type=118 (ANGLES) 69 71 72 60: 133 type=118 (ANGLES) 69 71 73 60: 134 type=120 (ANGLES) 69 71 74 60: 135 type=121 (ANGLES) 72 71 73 60: 136 type=118 (ANGLES) 72 71 74 60: 137 type=118 (ANGLES) 73 71 74 60: 138 type=118 (ANGLES) 71 74 75 60: 139 type=118 (ANGLES) 71 74 76 60: 140 type=120 (ANGLES) 71 74 77 60: 141 type=121 (ANGLES) 75 74 76 60: 142 type=118 (ANGLES) 75 74 77 60: 143 type=118 (ANGLES) 76 74 77 60: 144 type=118 (ANGLES) 74 77 78 60: 145 type=118 (ANGLES) 74 77 79 60: 146 type=117 (ANGLES) 74 77 80 60: 147 type=121 (ANGLES) 78 77 79 60: 148 type=116 (ANGLES) 78 77 80 60: 149 type=116 (ANGLES) 79 77 80 60: 150 type=134 (ANGLES) 77 80 81 60: 151 type=135 (ANGLES) 77 80 82 60: 152 type=133 (ANGLES) 81 80 82 60: 153 type=131 (ANGLES) 80 82 83 60: 154 type=131 (ANGLES) 80 82 86 60: 155 type=131 (ANGLES) 83 82 86 60: 156 type=133 (ANGLES) 82 83 84 60: 157 type=133 (ANGLES) 82 83 85 60: 158 type=133 (ANGLES) 84 83 85 60: 159 type=133 (ANGLES) 82 86 87 60: 160 type=133 (ANGLES) 82 86 88 60: 161 type=133 (ANGLES) 87 86 88 60: 162 type=122 (ANGLES) 69 89 90 60: 163 type=123 (ANGLES) 69 89 91 60: 164 type=124 (ANGLES) 90 89 91 60: 165 type=125 (ANGLES) 89 91 92 60: 166 type=126 (ANGLES) 89 91 93 60: 167 type=127 (ANGLES) 92 91 93 60: 168 type=116 (ANGLES) 91 93 94 60: 169 type=128 (ANGLES) 91 93 95 60: 170 type=129 (ANGLES) 91 93 100 60: 171 type=118 (ANGLES) 94 93 95 60: 172 type=116 (ANGLES) 94 93 100 60: 173 type=119 (ANGLES) 95 93 100 60: 174 type=118 (ANGLES) 93 95 96 60: 175 type=118 (ANGLES) 93 95 97 60: 176 type=136 (ANGLES) 93 95 98 60: 177 type=121 (ANGLES) 96 95 97 60: 178 type=116 (ANGLES) 96 95 98 60: 179 type=116 (ANGLES) 97 95 98 60: 180 type=137 (ANGLES) 95 98 99 60: 181 type=122 (ANGLES) 93 100 101 60: 182 type=123 (ANGLES) 93 100 102 60: 183 type=124 (ANGLES) 101 100 102 60: 184 type=125 (ANGLES) 100 102 103 60: 185 type=126 (ANGLES) 100 102 104 60: 186 type=127 (ANGLES) 103 102 104 60: 187 type=116 (ANGLES) 102 104 105 60: 188 type=128 (ANGLES) 102 104 106 60: 189 type=129 (ANGLES) 102 104 115 60: 190 type=118 (ANGLES) 105 104 106 60: 191 type=116 (ANGLES) 105 104 115 60: 192 type=119 (ANGLES) 106 104 115 60: 193 type=118 (ANGLES) 104 106 107 60: 194 type=118 (ANGLES) 104 106 108 60: 195 type=120 (ANGLES) 104 106 109 60: 196 type=121 (ANGLES) 107 106 108 60: 197 type=118 (ANGLES) 107 106 109 60: 198 type=118 (ANGLES) 108 106 109 60: 199 type=118 (ANGLES) 106 109 110 60: 200 type=118 (ANGLES) 106 109 111 60: 201 type=119 (ANGLES) 106 109 112 60: 202 type=121 (ANGLES) 110 109 111 60: 203 type=116 (ANGLES) 110 109 112 60: 204 type=116 (ANGLES) 111 109 112 60: 205 type=138 (ANGLES) 109 112 113 60: 206 type=138 (ANGLES) 109 112 114 60: 207 type=139 (ANGLES) 113 112 114 60: 208 type=122 (ANGLES) 104 115 116 60: 209 type=123 (ANGLES) 104 115 117 60: 210 type=124 (ANGLES) 116 115 117 60: 211 type=125 (ANGLES) 115 117 118 60: 212 type=126 (ANGLES) 115 117 119 60: 213 type=127 (ANGLES) 118 117 119 60: 214 type=116 (ANGLES) 117 119 120 60: 215 type=128 (ANGLES) 117 119 121 60: 216 type=129 (ANGLES) 117 119 134 60: 217 type=118 (ANGLES) 120 119 121 60: 218 type=116 (ANGLES) 120 119 134 60: 219 type=119 (ANGLES) 121 119 134 60: 220 type=118 (ANGLES) 119 121 122 60: 221 type=118 (ANGLES) 119 121 123 60: 222 type=120 (ANGLES) 119 121 124 60: 223 type=121 (ANGLES) 122 121 123 60: 224 type=118 (ANGLES) 122 121 124 60: 225 type=118 (ANGLES) 123 121 124 60: 226 type=118 (ANGLES) 121 124 125 60: 227 type=120 (ANGLES) 121 124 126 60: 228 type=120 (ANGLES) 121 124 130 60: 229 type=118 (ANGLES) 125 124 126 60: 230 type=118 (ANGLES) 125 124 130 60: 231 type=120 (ANGLES) 126 124 130 60: 232 type=118 (ANGLES) 124 126 127 60: 233 type=118 (ANGLES) 124 126 128 60: 234 type=118 (ANGLES) 124 126 129 60: 235 type=121 (ANGLES) 127 126 128 60: 236 type=121 (ANGLES) 127 126 129 60: 237 type=121 (ANGLES) 128 126 129 60: 238 type=118 (ANGLES) 124 130 131 60: 239 type=118 (ANGLES) 124 130 132 60: 240 type=118 (ANGLES) 124 130 133 60: 241 type=121 (ANGLES) 131 130 132 60: 242 type=121 (ANGLES) 131 130 133 60: 243 type=121 (ANGLES) 132 130 133 60: 244 type=122 (ANGLES) 119 134 135 60: 245 type=123 (ANGLES) 119 134 136 60: 246 type=124 (ANGLES) 135 134 136 60: 247 type=125 (ANGLES) 134 136 137 60: 248 type=126 (ANGLES) 134 136 138 60: 249 type=127 (ANGLES) 137 136 138 60: 250 type=116 (ANGLES) 136 138 139 60: 251 type=128 (ANGLES) 136 138 140 60: 252 type=129 (ANGLES) 136 138 144 60: 253 type=118 (ANGLES) 139 138 140 60: 254 type=116 (ANGLES) 139 138 144 60: 255 type=119 (ANGLES) 140 138 144 60: 256 type=118 (ANGLES) 138 140 141 60: 257 type=118 (ANGLES) 138 140 142 60: 258 type=118 (ANGLES) 138 140 143 60: 259 type=121 (ANGLES) 141 140 142 60: 260 type=121 (ANGLES) 141 140 143 60: 261 type=121 (ANGLES) 142 140 143 60: 262 type=122 (ANGLES) 138 144 145 60: 263 type=123 (ANGLES) 138 144 146 60: 264 type=124 (ANGLES) 145 144 146 60: 265 type=125 (ANGLES) 144 146 147 60: 266 type=126 (ANGLES) 144 146 148 60: 267 type=127 (ANGLES) 147 146 148 60: 268 type=116 (ANGLES) 146 148 149 60: 269 type=128 (ANGLES) 146 148 150 60: 270 type=129 (ANGLES) 146 148 154 60: 271 type=118 (ANGLES) 149 148 150 60: 272 type=116 (ANGLES) 149 148 154 60: 273 type=119 (ANGLES) 150 148 154 60: 274 type=118 (ANGLES) 148 150 151 60: 275 type=118 (ANGLES) 148 150 152 60: 276 type=118 (ANGLES) 148 150 153 60: 277 type=121 (ANGLES) 151 150 152 60: 278 type=121 (ANGLES) 151 150 153 60: 279 type=121 (ANGLES) 152 150 153 60: 280 type=122 (ANGLES) 148 154 155 60: G96Angle: 60: nr: 0 60: Restr. Angles: 60: nr: 0 60: Lin. Angle: 60: nr: 0 60: Bond-Cross: 60: nr: 0 60: BA-Cross: 60: nr: 0 60: U-B: 60: nr: 0 60: Quartic Angles: 60: nr: 0 60: Tab. Angles: 60: nr: 0 60: Proper Dih.: 60: nr: 145 60: iatoms: 60: 0 type=140 (PDIHS) 4 24 22 23 60: 1 type=141 (PDIHS) 22 26 24 25 60: 2 type=140 (PDIHS) 26 40 38 39 60: 3 type=141 (PDIHS) 38 42 40 41 60: 4 type=140 (PDIHS) 42 60 58 59 60: 5 type=142 (PDIHS) 44 47 50 48 60: 6 type=142 (PDIHS) 47 52 48 49 60: 7 type=142 (PDIHS) 47 54 50 51 60: 8 type=142 (PDIHS) 48 56 52 53 60: 9 type=142 (PDIHS) 50 56 54 55 60: 10 type=142 (PDIHS) 52 54 56 57 60: 11 type=141 (PDIHS) 58 62 60 61 60: 12 type=140 (PDIHS) 62 67 65 66 60: 13 type=141 (PDIHS) 65 69 67 68 60: 14 type=140 (PDIHS) 69 91 89 90 60: 15 type=141 (PDIHS) 77 82 80 81 60: 16 type=140 (PDIHS) 80 83 82 86 60: 17 type=141 (PDIHS) 82 84 83 85 60: 18 type=141 (PDIHS) 82 87 86 88 60: 19 type=141 (PDIHS) 89 93 91 92 60: 20 type=140 (PDIHS) 93 102 100 101 60: 21 type=141 (PDIHS) 100 104 102 103 60: 22 type=140 (PDIHS) 104 117 115 116 60: 23 type=140 (PDIHS) 109 113 112 114 60: 24 type=141 (PDIHS) 115 119 117 118 60: 25 type=140 (PDIHS) 119 136 134 135 60: 26 type=141 (PDIHS) 134 138 136 137 60: 27 type=140 (PDIHS) 138 146 144 145 60: 28 type=141 (PDIHS) 144 148 146 147 60: Ryckaert-Bell.: 60: nr: 1565 60: iatoms: 60: 0 type=143 (RBDIHS) 1 0 4 5 60: 1 type=144 (RBDIHS) 1 0 4 6 60: 2 type=144 (RBDIHS) 1 0 4 22 60: 3 type=143 (RBDIHS) 2 0 4 5 60: 4 type=144 (RBDIHS) 2 0 4 6 60: 5 type=144 (RBDIHS) 2 0 4 22 60: 6 type=143 (RBDIHS) 3 0 4 5 60: 7 type=144 (RBDIHS) 3 0 4 6 60: 8 type=144 (RBDIHS) 3 0 4 22 60: 9 type=145 (RBDIHS) 0 4 6 9 60: 10 type=146 (RBDIHS) 22 4 6 9 60: 11 type=147 (RBDIHS) 0 4 6 7 60: 12 type=147 (RBDIHS) 0 4 6 8 60: 13 type=148 (RBDIHS) 5 4 6 7 60: 14 type=148 (RBDIHS) 5 4 6 8 60: 15 type=148 (RBDIHS) 5 4 6 9 60: 16 type=149 (RBDIHS) 22 4 6 7 60: 17 type=149 (RBDIHS) 22 4 6 8 60: 18 type=150 (RBDIHS) 0 4 22 24 60: 19 type=151 (RBDIHS) 6 4 22 24 60: 20 type=148 (RBDIHS) 4 6 9 10 60: 21 type=148 (RBDIHS) 4 6 9 11 60: 22 type=152 (RBDIHS) 4 6 9 12 60: 23 type=148 (RBDIHS) 7 6 9 10 60: 24 type=148 (RBDIHS) 7 6 9 11 60: 25 type=148 (RBDIHS) 7 6 9 12 60: 26 type=148 (RBDIHS) 8 6 9 10 60: 27 type=148 (RBDIHS) 8 6 9 11 60: 28 type=148 (RBDIHS) 8 6 9 12 60: 29 type=148 (RBDIHS) 6 9 12 13 60: 30 type=148 (RBDIHS) 6 9 12 14 60: 31 type=152 (RBDIHS) 6 9 12 15 60: 32 type=148 (RBDIHS) 10 9 12 13 60: 33 type=148 (RBDIHS) 10 9 12 14 60: 34 type=148 (RBDIHS) 10 9 12 15 60: 35 type=148 (RBDIHS) 11 9 12 13 60: 36 type=148 (RBDIHS) 11 9 12 14 60: 37 type=148 (RBDIHS) 11 9 12 15 60: 38 type=148 (RBDIHS) 9 12 15 16 60: 39 type=148 (RBDIHS) 9 12 15 17 60: 40 type=153 (RBDIHS) 9 12 15 18 60: 41 type=148 (RBDIHS) 13 12 15 16 60: 42 type=148 (RBDIHS) 13 12 15 17 60: 43 type=154 (RBDIHS) 13 12 15 18 60: 44 type=148 (RBDIHS) 14 12 15 16 60: 45 type=148 (RBDIHS) 14 12 15 17 60: 46 type=154 (RBDIHS) 14 12 15 18 60: 47 type=144 (RBDIHS) 12 15 18 19 60: 48 type=144 (RBDIHS) 12 15 18 20 60: 49 type=144 (RBDIHS) 12 15 18 21 60: 50 type=143 (RBDIHS) 16 15 18 19 60: 51 type=143 (RBDIHS) 16 15 18 20 60: 52 type=143 (RBDIHS) 16 15 18 21 60: 53 type=143 (RBDIHS) 17 15 18 19 60: 54 type=143 (RBDIHS) 17 15 18 20 60: 55 type=143 (RBDIHS) 17 15 18 21 60: 56 type=155 (RBDIHS) 4 22 24 25 60: 57 type=156 (RBDIHS) 4 22 24 26 60: 58 type=155 (RBDIHS) 23 22 24 25 60: 59 type=157 (RBDIHS) 23 22 24 26 60: 60 type=158 (RBDIHS) 22 24 26 28 60: 61 type=159 (RBDIHS) 22 24 26 38 60: 62 type=160 (RBDIHS) 24 26 28 30 60: 63 type=160 (RBDIHS) 24 26 28 34 60: 64 type=161 (RBDIHS) 38 26 28 30 60: 65 type=161 (RBDIHS) 38 26 28 34 60: 66 type=147 (RBDIHS) 24 26 28 29 60: 67 type=148 (RBDIHS) 27 26 28 29 60: 68 type=148 (RBDIHS) 27 26 28 30 60: 69 type=148 (RBDIHS) 27 26 28 34 60: 70 type=149 (RBDIHS) 38 26 28 29 60: 71 type=150 (RBDIHS) 24 26 38 40 60: 72 type=151 (RBDIHS) 28 26 38 40 60: 73 type=148 (RBDIHS) 26 28 30 31 60: 74 type=148 (RBDIHS) 26 28 30 32 60: 75 type=148 (RBDIHS) 26 28 30 33 60: 76 type=148 (RBDIHS) 29 28 30 31 60: 77 type=148 (RBDIHS) 29 28 30 32 60: 78 type=148 (RBDIHS) 29 28 30 33 60: 79 type=148 (RBDIHS) 34 28 30 31 60: 80 type=148 (RBDIHS) 34 28 30 32 60: 81 type=148 (RBDIHS) 34 28 30 33 60: 82 type=148 (RBDIHS) 26 28 34 35 60: 83 type=148 (RBDIHS) 26 28 34 36 60: 84 type=148 (RBDIHS) 26 28 34 37 60: 85 type=148 (RBDIHS) 29 28 34 35 60: 86 type=148 (RBDIHS) 29 28 34 36 60: 87 type=148 (RBDIHS) 29 28 34 37 60: 88 type=148 (RBDIHS) 30 28 34 35 60: 89 type=148 (RBDIHS) 30 28 34 36 60: 90 type=148 (RBDIHS) 30 28 34 37 60: 91 type=155 (RBDIHS) 26 38 40 41 60: 92 type=156 (RBDIHS) 26 38 40 42 60: 93 type=155 (RBDIHS) 39 38 40 41 60: 94 type=157 (RBDIHS) 39 38 40 42 60: 95 type=158 (RBDIHS) 38 40 42 44 60: 96 type=159 (RBDIHS) 38 40 42 58 60: 97 type=147 (RBDIHS) 40 42 44 45 60: 98 type=147 (RBDIHS) 40 42 44 46 60: 99 type=162 (RBDIHS) 40 42 44 47 60: 100 type=148 (RBDIHS) 43 42 44 45 60: 101 type=148 (RBDIHS) 43 42 44 46 60: 102 type=163 (RBDIHS) 43 42 44 47 60: 103 type=149 (RBDIHS) 58 42 44 45 60: 104 type=149 (RBDIHS) 58 42 44 46 60: 105 type=164 (RBDIHS) 58 42 44 47 60: 106 type=150 (RBDIHS) 40 42 58 60 60: 107 type=151 (RBDIHS) 44 42 58 60 60: 108 type=165 (RBDIHS) 44 47 48 49 60: 109 type=165 (RBDIHS) 44 47 48 52 60: 110 type=165 (RBDIHS) 50 47 48 49 60: 111 type=165 (RBDIHS) 50 47 48 52 60: 112 type=165 (RBDIHS) 44 47 50 51 60: 113 type=165 (RBDIHS) 44 47 50 54 60: 114 type=165 (RBDIHS) 48 47 50 51 60: 115 type=165 (RBDIHS) 48 47 50 54 60: 116 type=165 (RBDIHS) 47 48 52 53 60: 117 type=165 (RBDIHS) 47 48 52 56 60: 118 type=165 (RBDIHS) 49 48 52 53 60: 119 type=165 (RBDIHS) 49 48 52 56 60: 120 type=165 (RBDIHS) 47 50 54 55 60: 121 type=165 (RBDIHS) 47 50 54 56 60: 122 type=165 (RBDIHS) 51 50 54 55 60: 123 type=165 (RBDIHS) 51 50 54 56 60: 124 type=165 (RBDIHS) 48 52 56 54 60: 125 type=165 (RBDIHS) 48 52 56 57 60: 126 type=165 (RBDIHS) 53 52 56 54 60: 127 type=165 (RBDIHS) 53 52 56 57 60: 128 type=165 (RBDIHS) 50 54 56 52 60: 129 type=165 (RBDIHS) 50 54 56 57 60: 130 type=165 (RBDIHS) 55 54 56 52 60: 131 type=165 (RBDIHS) 55 54 56 57 60: 132 type=155 (RBDIHS) 42 58 60 61 60: 133 type=156 (RBDIHS) 42 58 60 62 60: 134 type=155 (RBDIHS) 59 58 60 61 60: 135 type=157 (RBDIHS) 59 58 60 62 60: 136 type=159 (RBDIHS) 58 60 62 65 60: 137 type=150 (RBDIHS) 60 62 65 67 60: 138 type=155 (RBDIHS) 62 65 67 68 60: 139 type=156 (RBDIHS) 62 65 67 69 60: 140 type=155 (RBDIHS) 66 65 67 68 60: 141 type=157 (RBDIHS) 66 65 67 69 60: 142 type=158 (RBDIHS) 65 67 69 71 60: 143 type=159 (RBDIHS) 65 67 69 89 60: 144 type=166 (RBDIHS) 67 69 71 74 60: 145 type=167 (RBDIHS) 89 69 71 74 60: 146 type=147 (RBDIHS) 67 69 71 72 60: 147 type=147 (RBDIHS) 67 69 71 73 60: 148 type=148 (RBDIHS) 70 69 71 72 60: 149 type=148 (RBDIHS) 70 69 71 73 60: 150 type=148 (RBDIHS) 70 69 71 74 60: 151 type=149 (RBDIHS) 89 69 71 72 60: 152 type=149 (RBDIHS) 89 69 71 73 60: 153 type=150 (RBDIHS) 67 69 89 91 60: 154 type=151 (RBDIHS) 71 69 89 91 60: 155 type=148 (RBDIHS) 69 71 74 75 60: 156 type=148 (RBDIHS) 69 71 74 76 60: 157 type=152 (RBDIHS) 69 71 74 77 60: 158 type=148 (RBDIHS) 72 71 74 75 60: 159 type=148 (RBDIHS) 72 71 74 76 60: 160 type=148 (RBDIHS) 72 71 74 77 60: 161 type=148 (RBDIHS) 73 71 74 75 60: 162 type=148 (RBDIHS) 73 71 74 76 60: 163 type=148 (RBDIHS) 73 71 74 77 60: 164 type=148 (RBDIHS) 71 74 77 78 60: 165 type=148 (RBDIHS) 71 74 77 79 60: 166 type=153 (RBDIHS) 71 74 77 80 60: 167 type=148 (RBDIHS) 75 74 77 78 60: 168 type=148 (RBDIHS) 75 74 77 79 60: 169 type=168 (RBDIHS) 75 74 77 80 60: 170 type=148 (RBDIHS) 76 74 77 78 60: 171 type=148 (RBDIHS) 76 74 77 79 60: 172 type=168 (RBDIHS) 76 74 77 80 60: 173 type=169 (RBDIHS) 74 77 80 81 60: 174 type=170 (RBDIHS) 74 77 80 82 60: 175 type=171 (RBDIHS) 78 77 80 82 60: 176 type=171 (RBDIHS) 79 77 80 82 60: 177 type=172 (RBDIHS) 77 80 82 83 60: 178 type=172 (RBDIHS) 77 80 82 86 60: 179 type=173 (RBDIHS) 81 80 82 83 60: 180 type=173 (RBDIHS) 81 80 82 86 60: 181 type=173 (RBDIHS) 80 82 83 84 60: 182 type=173 (RBDIHS) 80 82 83 85 60: 183 type=173 (RBDIHS) 86 82 83 84 60: 184 type=173 (RBDIHS) 86 82 83 85 60: 185 type=173 (RBDIHS) 80 82 86 87 60: 186 type=173 (RBDIHS) 80 82 86 88 60: 187 type=173 (RBDIHS) 83 82 86 87 60: 188 type=173 (RBDIHS) 83 82 86 88 60: 189 type=155 (RBDIHS) 69 89 91 92 60: 190 type=156 (RBDIHS) 69 89 91 93 60: 191 type=155 (RBDIHS) 90 89 91 92 60: 192 type=157 (RBDIHS) 90 89 91 93 60: 193 type=158 (RBDIHS) 89 91 93 95 60: 194 type=159 (RBDIHS) 89 91 93 100 60: 195 type=174 (RBDIHS) 91 93 95 98 60: 196 type=175 (RBDIHS) 100 93 95 98 60: 197 type=147 (RBDIHS) 91 93 95 96 60: 198 type=147 (RBDIHS) 91 93 95 97 60: 199 type=148 (RBDIHS) 94 93 95 96 60: 200 type=148 (RBDIHS) 94 93 95 97 60: 201 type=176 (RBDIHS) 94 93 95 98 60: 202 type=149 (RBDIHS) 100 93 95 96 60: 203 type=149 (RBDIHS) 100 93 95 97 60: 204 type=150 (RBDIHS) 91 93 100 102 60: 205 type=151 (RBDIHS) 95 93 100 102 60: 206 type=177 (RBDIHS) 93 95 98 99 60: 207 type=178 (RBDIHS) 96 95 98 99 60: 208 type=178 (RBDIHS) 97 95 98 99 60: 209 type=155 (RBDIHS) 93 100 102 103 60: 210 type=156 (RBDIHS) 93 100 102 104 60: 211 type=155 (RBDIHS) 101 100 102 103 60: 212 type=157 (RBDIHS) 101 100 102 104 60: 213 type=158 (RBDIHS) 100 102 104 106 60: 214 type=159 (RBDIHS) 100 102 104 115 60: 215 type=179 (RBDIHS) 102 104 106 109 60: 216 type=180 (RBDIHS) 115 104 106 109 60: 217 type=147 (RBDIHS) 102 104 106 107 60: 218 type=147 (RBDIHS) 102 104 106 108 60: 219 type=148 (RBDIHS) 105 104 106 107 60: 220 type=148 (RBDIHS) 105 104 106 108 60: 221 type=148 (RBDIHS) 105 104 106 109 60: 222 type=149 (RBDIHS) 115 104 106 107 60: 223 type=149 (RBDIHS) 115 104 106 108 60: 224 type=150 (RBDIHS) 102 104 115 117 60: 225 type=151 (RBDIHS) 106 104 115 117 60: 226 type=148 (RBDIHS) 104 106 109 110 60: 227 type=148 (RBDIHS) 104 106 109 111 60: 228 type=181 (RBDIHS) 104 106 109 112 60: 229 type=148 (RBDIHS) 107 106 109 110 60: 230 type=148 (RBDIHS) 107 106 109 111 60: 231 type=182 (RBDIHS) 107 106 109 112 60: 232 type=148 (RBDIHS) 108 106 109 110 60: 233 type=148 (RBDIHS) 108 106 109 111 60: 234 type=182 (RBDIHS) 108 106 109 112 60: 235 type=183 (RBDIHS) 106 109 112 113 60: 236 type=183 (RBDIHS) 106 109 112 114 60: 237 type=155 (RBDIHS) 104 115 117 118 60: 238 type=156 (RBDIHS) 104 115 117 119 60: 239 type=155 (RBDIHS) 116 115 117 118 60: 240 type=157 (RBDIHS) 116 115 117 119 60: 241 type=158 (RBDIHS) 115 117 119 121 60: 242 type=159 (RBDIHS) 115 117 119 134 60: 243 type=184 (RBDIHS) 117 119 121 124 60: 244 type=185 (RBDIHS) 134 119 121 124 60: 245 type=147 (RBDIHS) 117 119 121 122 60: 246 type=147 (RBDIHS) 117 119 121 123 60: 247 type=148 (RBDIHS) 120 119 121 122 60: 248 type=148 (RBDIHS) 120 119 121 123 60: 249 type=148 (RBDIHS) 120 119 121 124 60: 250 type=149 (RBDIHS) 134 119 121 122 60: 251 type=149 (RBDIHS) 134 119 121 123 60: 252 type=150 (RBDIHS) 117 119 134 136 60: 253 type=151 (RBDIHS) 121 119 134 136 60: 254 type=148 (RBDIHS) 119 121 124 125 60: 255 type=152 (RBDIHS) 119 121 124 126 60: 256 type=152 (RBDIHS) 119 121 124 130 60: 257 type=148 (RBDIHS) 122 121 124 125 60: 258 type=148 (RBDIHS) 122 121 124 126 60: 259 type=148 (RBDIHS) 122 121 124 130 60: 260 type=148 (RBDIHS) 123 121 124 125 60: 261 type=148 (RBDIHS) 123 121 124 126 60: 262 type=148 (RBDIHS) 123 121 124 130 60: 263 type=148 (RBDIHS) 121 124 126 127 60: 264 type=148 (RBDIHS) 121 124 126 128 60: 265 type=148 (RBDIHS) 121 124 126 129 60: 266 type=148 (RBDIHS) 125 124 126 127 60: 267 type=148 (RBDIHS) 125 124 126 128 60: 268 type=148 (RBDIHS) 125 124 126 129 60: 269 type=148 (RBDIHS) 130 124 126 127 60: 270 type=148 (RBDIHS) 130 124 126 128 60: 271 type=148 (RBDIHS) 130 124 126 129 60: 272 type=148 (RBDIHS) 121 124 130 131 60: 273 type=148 (RBDIHS) 121 124 130 132 60: 274 type=148 (RBDIHS) 121 124 130 133 60: 275 type=148 (RBDIHS) 125 124 130 131 60: 276 type=148 (RBDIHS) 125 124 130 132 60: 277 type=148 (RBDIHS) 125 124 130 133 60: 278 type=148 (RBDIHS) 126 124 130 131 60: 279 type=148 (RBDIHS) 126 124 130 132 60: 280 type=148 (RBDIHS) 126 124 130 133 60: 281 type=155 (RBDIHS) 119 134 136 137 60: 282 type=156 (RBDIHS) 119 134 136 138 60: 283 type=155 (RBDIHS) 135 134 136 137 60: 284 type=157 (RBDIHS) 135 134 136 138 60: 285 type=158 (RBDIHS) 134 136 138 140 60: 286 type=159 (RBDIHS) 134 136 138 144 60: 287 type=147 (RBDIHS) 136 138 140 141 60: 288 type=147 (RBDIHS) 136 138 140 142 60: 289 type=147 (RBDIHS) 136 138 140 143 60: 290 type=148 (RBDIHS) 139 138 140 141 60: 291 type=148 (RBDIHS) 139 138 140 142 60: 292 type=148 (RBDIHS) 139 138 140 143 60: 293 type=149 (RBDIHS) 144 138 140 141 60: 294 type=149 (RBDIHS) 144 138 140 142 60: 295 type=149 (RBDIHS) 144 138 140 143 60: 296 type=150 (RBDIHS) 136 138 144 146 60: 297 type=151 (RBDIHS) 140 138 144 146 60: 298 type=155 (RBDIHS) 138 144 146 147 60: 299 type=156 (RBDIHS) 138 144 146 148 60: 300 type=155 (RBDIHS) 145 144 146 147 60: 301 type=157 (RBDIHS) 145 144 146 148 60: 302 type=158 (RBDIHS) 144 146 148 150 60: 303 type=159 (RBDIHS) 144 146 148 154 60: 304 type=147 (RBDIHS) 146 148 150 151 60: 305 type=147 (RBDIHS) 146 148 150 152 60: 306 type=147 (RBDIHS) 146 148 150 153 60: 307 type=148 (RBDIHS) 149 148 150 151 60: 308 type=148 (RBDIHS) 149 148 150 152 60: 309 type=148 (RBDIHS) 149 148 150 153 60: 310 type=149 (RBDIHS) 154 148 150 151 60: 311 type=149 (RBDIHS) 154 148 150 152 60: 312 type=149 (RBDIHS) 154 148 150 153 60: Restr. Dih.: 60: nr: 0 60: CBT Dih.: 60: nr: 0 60: Fourier Dih.: 60: nr: 0 60: Improper Dih.: 60: nr: 0 60: Per. Imp. Dih.: 60: nr: 0 60: Tab. Dih.: 60: nr: 0 60: CMAP Dih.: 60: nr: 0 60: GB 1-2 Pol.: 60: nr: 0 60: GB 1-3 Pol.: 60: nr: 0 60: GB 1-4 Pol.: 60: nr: 0 60: GB Polariz.: 60: nr: 0 60: Nonpolar Sol.: 60: nr: 0 60: LJ-14: 60: nr: 1197 60: iatoms: 60: 0 type=186 (LJ14) 0 7 60: 1 type=186 (LJ14) 0 8 60: 2 type=187 (LJ14) 0 9 60: 3 type=188 (LJ14) 0 23 60: 4 type=189 (LJ14) 0 24 60: 5 type=190 (LJ14) 1 5 60: 6 type=190 (LJ14) 1 6 60: 7 type=190 (LJ14) 1 22 60: 8 type=190 (LJ14) 2 5 60: 9 type=190 (LJ14) 2 6 60: 10 type=190 (LJ14) 2 22 60: 11 type=190 (LJ14) 3 5 60: 12 type=190 (LJ14) 3 6 60: 13 type=190 (LJ14) 3 22 60: 14 type=191 (LJ14) 4 10 60: 15 type=191 (LJ14) 4 11 60: 16 type=192 (LJ14) 4 12 60: 17 type=190 (LJ14) 4 25 60: 18 type=192 (LJ14) 4 26 60: 19 type=193 (LJ14) 5 7 60: 20 type=193 (LJ14) 5 8 60: 21 type=191 (LJ14) 5 9 60: 22 type=194 (LJ14) 5 23 60: 23 type=186 (LJ14) 5 24 60: 24 type=191 (LJ14) 6 13 60: 25 type=191 (LJ14) 6 14 60: 26 type=192 (LJ14) 6 15 60: 27 type=195 (LJ14) 6 23 60: 28 type=187 (LJ14) 6 24 60: 29 type=193 (LJ14) 7 10 60: 30 type=193 (LJ14) 7 11 60: 31 type=191 (LJ14) 7 12 60: 32 type=196 (LJ14) 7 22 60: 33 type=193 (LJ14) 8 10 60: 34 type=193 (LJ14) 8 11 60: 35 type=191 (LJ14) 8 12 60: 36 type=196 (LJ14) 8 22 60: 37 type=191 (LJ14) 9 16 60: 38 type=191 (LJ14) 9 17 60: 39 type=187 (LJ14) 9 18 60: 40 type=197 (LJ14) 9 22 60: 41 type=193 (LJ14) 10 13 60: 42 type=193 (LJ14) 10 14 60: 43 type=191 (LJ14) 10 15 60: 44 type=193 (LJ14) 11 13 60: 45 type=193 (LJ14) 11 14 60: 46 type=191 (LJ14) 11 15 60: 47 type=190 (LJ14) 12 19 60: 48 type=190 (LJ14) 12 20 60: 49 type=190 (LJ14) 12 21 60: 50 type=193 (LJ14) 13 16 60: 51 type=193 (LJ14) 13 17 60: 52 type=186 (LJ14) 13 18 60: 53 type=193 (LJ14) 14 16 60: 54 type=193 (LJ14) 14 17 60: 55 type=186 (LJ14) 14 18 60: 56 type=190 (LJ14) 16 19 60: 57 type=190 (LJ14) 16 20 60: 58 type=190 (LJ14) 16 21 60: 59 type=190 (LJ14) 17 19 60: 60 type=190 (LJ14) 17 20 60: 61 type=190 (LJ14) 17 21 60: 62 type=196 (LJ14) 22 27 60: 63 type=197 (LJ14) 22 28 60: 64 type=198 (LJ14) 22 38 60: 65 type=190 (LJ14) 23 25 60: 66 type=195 (LJ14) 23 26 60: 67 type=186 (LJ14) 24 29 60: 68 type=187 (LJ14) 24 30 60: 69 type=187 (LJ14) 24 34 60: 70 type=188 (LJ14) 24 39 60: 71 type=189 (LJ14) 24 40 60: 72 type=190 (LJ14) 25 27 60: 73 type=190 (LJ14) 25 28 60: 74 type=190 (LJ14) 25 38 60: 75 type=191 (LJ14) 26 31 60: 76 type=191 (LJ14) 26 32 60: 77 type=191 (LJ14) 26 33 60: 78 type=191 (LJ14) 26 35 60: 79 type=191 (LJ14) 26 36 60: 80 type=191 (LJ14) 26 37 60: 81 type=190 (LJ14) 26 41 60: 82 type=192 (LJ14) 26 42 60: 83 type=193 (LJ14) 27 29 60: 84 type=191 (LJ14) 27 30 60: 85 type=191 (LJ14) 27 34 60: 86 type=194 (LJ14) 27 39 60: 87 type=186 (LJ14) 27 40 60: 88 type=195 (LJ14) 28 39 60: 89 type=187 (LJ14) 28 40 60: 90 type=193 (LJ14) 29 31 60: 91 type=193 (LJ14) 29 32 60: 92 type=193 (LJ14) 29 33 60: 93 type=193 (LJ14) 29 35 60: 94 type=193 (LJ14) 29 36 60: 95 type=193 (LJ14) 29 37 60: 96 type=196 (LJ14) 29 38 60: 97 type=191 (LJ14) 30 35 60: 98 type=191 (LJ14) 30 36 60: 99 type=191 (LJ14) 30 37 60: 100 type=197 (LJ14) 30 38 60: 101 type=191 (LJ14) 31 34 60: 102 type=191 (LJ14) 32 34 60: 103 type=191 (LJ14) 33 34 60: 104 type=197 (LJ14) 34 38 60: 105 type=196 (LJ14) 38 43 60: 106 type=197 (LJ14) 38 44 60: 107 type=198 (LJ14) 38 58 60: 108 type=190 (LJ14) 39 41 60: 109 type=195 (LJ14) 39 42 60: 110 type=186 (LJ14) 40 45 60: 111 type=186 (LJ14) 40 46 60: 112 type=199 (LJ14) 40 47 60: 113 type=188 (LJ14) 40 59 60: 114 type=189 (LJ14) 40 60 60: 115 type=190 (LJ14) 41 43 60: 116 type=190 (LJ14) 41 44 60: 117 type=190 (LJ14) 41 58 60: 118 type=200 (LJ14) 42 48 60: 119 type=200 (LJ14) 42 50 60: 120 type=190 (LJ14) 42 61 60: 121 type=192 (LJ14) 42 62 60: 122 type=193 (LJ14) 43 45 60: 123 type=193 (LJ14) 43 46 60: 124 type=201 (LJ14) 43 47 60: 125 type=194 (LJ14) 43 59 60: 126 type=186 (LJ14) 43 60 60: 127 type=202 (LJ14) 44 49 60: 128 type=202 (LJ14) 44 51 60: 129 type=200 (LJ14) 44 52 60: 130 type=200 (LJ14) 44 54 60: 131 type=195 (LJ14) 44 59 60: 132 type=187 (LJ14) 44 60 60: 133 type=201 (LJ14) 45 48 60: 134 type=201 (LJ14) 45 50 60: 135 type=196 (LJ14) 45 58 60: 136 type=201 (LJ14) 46 48 60: 137 type=201 (LJ14) 46 50 60: 138 type=196 (LJ14) 46 58 60: 139 type=203 (LJ14) 47 53 60: 140 type=203 (LJ14) 47 55 60: 141 type=204 (LJ14) 47 56 60: 142 type=205 (LJ14) 47 58 60: 143 type=203 (LJ14) 48 51 60: 144 type=204 (LJ14) 48 54 60: 145 type=203 (LJ14) 48 57 60: 146 type=203 (LJ14) 49 50 60: 147 type=206 (LJ14) 49 53 60: 148 type=203 (LJ14) 49 56 60: 149 type=204 (LJ14) 50 52 60: 150 type=203 (LJ14) 50 57 60: 151 type=206 (LJ14) 51 55 60: 152 type=203 (LJ14) 51 56 60: 153 type=203 (LJ14) 52 55 60: 154 type=203 (LJ14) 53 54 60: 155 type=206 (LJ14) 53 57 60: 156 type=206 (LJ14) 55 57 60: 157 type=196 (LJ14) 58 63 60: 158 type=196 (LJ14) 58 64 60: 159 type=198 (LJ14) 58 65 60: 160 type=190 (LJ14) 59 61 60: 161 type=195 (LJ14) 59 62 60: 162 type=188 (LJ14) 60 66 60: 163 type=189 (LJ14) 60 67 60: 164 type=190 (LJ14) 61 63 60: 165 type=190 (LJ14) 61 64 60: 166 type=190 (LJ14) 61 65 60: 167 type=190 (LJ14) 62 68 60: 168 type=192 (LJ14) 62 69 60: 169 type=194 (LJ14) 63 66 60: 170 type=186 (LJ14) 63 67 60: 171 type=194 (LJ14) 64 66 60: 172 type=186 (LJ14) 64 67 60: 173 type=196 (LJ14) 65 70 60: 174 type=197 (LJ14) 65 71 60: 175 type=198 (LJ14) 65 89 60: 176 type=190 (LJ14) 66 68 60: 177 type=195 (LJ14) 66 69 60: 178 type=186 (LJ14) 67 72 60: 179 type=186 (LJ14) 67 73 60: 180 type=187 (LJ14) 67 74 60: 181 type=188 (LJ14) 67 90 60: 182 type=189 (LJ14) 67 91 60: 183 type=190 (LJ14) 68 70 60: 184 type=190 (LJ14) 68 71 60: 185 type=190 (LJ14) 68 89 60: 186 type=191 (LJ14) 69 75 60: 187 type=191 (LJ14) 69 76 60: 188 type=192 (LJ14) 69 77 60: 189 type=190 (LJ14) 69 92 60: 190 type=192 (LJ14) 69 93 60: 191 type=193 (LJ14) 70 72 60: 192 type=193 (LJ14) 70 73 60: 193 type=191 (LJ14) 70 74 60: 194 type=194 (LJ14) 70 90 60: 195 type=186 (LJ14) 70 91 60: 196 type=191 (LJ14) 71 78 60: 197 type=191 (LJ14) 71 79 60: 198 type=187 (LJ14) 71 80 60: 199 type=195 (LJ14) 71 90 60: 200 type=187 (LJ14) 71 91 60: 201 type=193 (LJ14) 72 75 60: 202 type=193 (LJ14) 72 76 60: 203 type=191 (LJ14) 72 77 60: 204 type=196 (LJ14) 72 89 60: 205 type=193 (LJ14) 73 75 60: 206 type=193 (LJ14) 73 76 60: 207 type=191 (LJ14) 73 77 60: 208 type=196 (LJ14) 73 89 60: 209 type=190 (LJ14) 74 81 60: 210 type=207 (LJ14) 74 82 60: 211 type=197 (LJ14) 74 89 60: 212 type=193 (LJ14) 75 78 60: 213 type=193 (LJ14) 75 79 60: 214 type=186 (LJ14) 75 80 60: 215 type=193 (LJ14) 76 78 60: 216 type=193 (LJ14) 76 79 60: 217 type=186 (LJ14) 76 80 60: 218 type=187 (LJ14) 77 83 60: 219 type=187 (LJ14) 77 86 60: 220 type=190 (LJ14) 78 81 60: 221 type=208 (LJ14) 78 82 60: 222 type=190 (LJ14) 79 81 60: 223 type=208 (LJ14) 79 82 60: 224 type=190 (LJ14) 80 84 60: 225 type=190 (LJ14) 80 85 60: 226 type=190 (LJ14) 80 87 60: 227 type=190 (LJ14) 80 88 60: 228 type=190 (LJ14) 81 83 60: 229 type=190 (LJ14) 81 86 60: 230 type=190 (LJ14) 83 87 60: 231 type=190 (LJ14) 83 88 60: 232 type=190 (LJ14) 84 86 60: 233 type=190 (LJ14) 85 86 60: 234 type=196 (LJ14) 89 94 60: 235 type=197 (LJ14) 89 95 60: 236 type=198 (LJ14) 89 100 60: 237 type=190 (LJ14) 90 92 60: 238 type=195 (LJ14) 90 93 60: 239 type=186 (LJ14) 91 96 60: 240 type=186 (LJ14) 91 97 60: 241 type=209 (LJ14) 91 98 60: 242 type=188 (LJ14) 91 101 60: 243 type=189 (LJ14) 91 102 60: 244 type=190 (LJ14) 92 94 60: 245 type=190 (LJ14) 92 95 60: 246 type=190 (LJ14) 92 100 60: 247 type=190 (LJ14) 93 99 60: 248 type=190 (LJ14) 93 103 60: 249 type=192 (LJ14) 93 104 60: 250 type=193 (LJ14) 94 96 60: 251 type=193 (LJ14) 94 97 60: 252 type=210 (LJ14) 94 98 60: 253 type=194 (LJ14) 94 101 60: 254 type=186 (LJ14) 94 102 60: 255 type=195 (LJ14) 95 101 60: 256 type=187 (LJ14) 95 102 60: 257 type=190 (LJ14) 96 99 60: 258 type=196 (LJ14) 96 100 60: 259 type=190 (LJ14) 97 99 60: 260 type=196 (LJ14) 97 100 60: 261 type=211 (LJ14) 98 100 60: 262 type=196 (LJ14) 100 105 60: 263 type=197 (LJ14) 100 106 60: 264 type=198 (LJ14) 100 115 60: 265 type=190 (LJ14) 101 103 60: 266 type=195 (LJ14) 101 104 60: 267 type=186 (LJ14) 102 107 60: 268 type=186 (LJ14) 102 108 60: 269 type=187 (LJ14) 102 109 60: 270 type=188 (LJ14) 102 116 60: 271 type=189 (LJ14) 102 117 60: 272 type=190 (LJ14) 103 105 60: 273 type=190 (LJ14) 103 106 60: 274 type=190 (LJ14) 103 115 60: 275 type=191 (LJ14) 104 110 60: 276 type=191 (LJ14) 104 111 60: 277 type=197 (LJ14) 104 112 60: 278 type=190 (LJ14) 104 118 60: 279 type=192 (LJ14) 104 119 60: 280 type=193 (LJ14) 105 107 60: 281 type=193 (LJ14) 105 108 60: 282 type=191 (LJ14) 105 109 60: 283 type=194 (LJ14) 105 116 60: 284 type=186 (LJ14) 105 117 60: 285 type=195 (LJ14) 106 113 60: 286 type=195 (LJ14) 106 114 60: 287 type=195 (LJ14) 106 116 60: 288 type=187 (LJ14) 106 117 60: 289 type=193 (LJ14) 107 110 60: 290 type=193 (LJ14) 107 111 60: 291 type=196 (LJ14) 107 112 60: 292 type=196 (LJ14) 107 115 60: 293 type=193 (LJ14) 108 110 60: 294 type=193 (LJ14) 108 111 60: 295 type=196 (LJ14) 108 112 60: 296 type=196 (LJ14) 108 115 60: 297 type=197 (LJ14) 109 115 60: 298 type=194 (LJ14) 110 113 60: 299 type=194 (LJ14) 110 114 60: 300 type=194 (LJ14) 111 113 60: 301 type=194 (LJ14) 111 114 60: 302 type=196 (LJ14) 115 120 60: 303 type=197 (LJ14) 115 121 60: 304 type=198 (LJ14) 115 134 60: 305 type=190 (LJ14) 116 118 60: 306 type=195 (LJ14) 116 119 60: 307 type=186 (LJ14) 117 122 60: 308 type=186 (LJ14) 117 123 60: 309 type=187 (LJ14) 117 124 60: 310 type=188 (LJ14) 117 135 60: 311 type=189 (LJ14) 117 136 60: 312 type=190 (LJ14) 118 120 60: 313 type=190 (LJ14) 118 121 60: 314 type=190 (LJ14) 118 134 60: 315 type=191 (LJ14) 119 125 60: 316 type=192 (LJ14) 119 126 60: 317 type=192 (LJ14) 119 130 60: 318 type=190 (LJ14) 119 137 60: 319 type=192 (LJ14) 119 138 60: 320 type=193 (LJ14) 120 122 60: 321 type=193 (LJ14) 120 123 60: 322 type=191 (LJ14) 120 124 60: 323 type=194 (LJ14) 120 135 60: 324 type=186 (LJ14) 120 136 60: 325 type=191 (LJ14) 121 127 60: 326 type=191 (LJ14) 121 128 60: 327 type=191 (LJ14) 121 129 60: 328 type=191 (LJ14) 121 131 60: 329 type=191 (LJ14) 121 132 60: 330 type=191 (LJ14) 121 133 60: 331 type=195 (LJ14) 121 135 60: 332 type=187 (LJ14) 121 136 60: 333 type=193 (LJ14) 122 125 60: 334 type=191 (LJ14) 122 126 60: 335 type=191 (LJ14) 122 130 60: 336 type=196 (LJ14) 122 134 60: 337 type=193 (LJ14) 123 125 60: 338 type=191 (LJ14) 123 126 60: 339 type=191 (LJ14) 123 130 60: 340 type=196 (LJ14) 123 134 60: 341 type=197 (LJ14) 124 134 60: 342 type=193 (LJ14) 125 127 60: 343 type=193 (LJ14) 125 128 60: 344 type=193 (LJ14) 125 129 60: 345 type=193 (LJ14) 125 131 60: 346 type=193 (LJ14) 125 132 60: 347 type=193 (LJ14) 125 133 60: 348 type=191 (LJ14) 126 131 60: 349 type=191 (LJ14) 126 132 60: 350 type=191 (LJ14) 126 133 60: 351 type=191 (LJ14) 127 130 60: 352 type=191 (LJ14) 128 130 60: 353 type=191 (LJ14) 129 130 60: 354 type=196 (LJ14) 134 139 60: 355 type=197 (LJ14) 134 140 60: 356 type=198 (LJ14) 134 144 60: 357 type=190 (LJ14) 135 137 60: 358 type=195 (LJ14) 135 138 60: 359 type=186 (LJ14) 136 141 60: 360 type=186 (LJ14) 136 142 60: 361 type=186 (LJ14) 136 143 60: 362 type=188 (LJ14) 136 145 60: 363 type=189 (LJ14) 136 146 60: 364 type=190 (LJ14) 137 139 60: 365 type=190 (LJ14) 137 140 60: 366 type=190 (LJ14) 137 144 60: 367 type=190 (LJ14) 138 147 60: 368 type=192 (LJ14) 138 148 60: 369 type=193 (LJ14) 139 141 60: 370 type=193 (LJ14) 139 142 60: 371 type=193 (LJ14) 139 143 60: 372 type=194 (LJ14) 139 145 60: 373 type=186 (LJ14) 139 146 60: 374 type=195 (LJ14) 140 145 60: 375 type=187 (LJ14) 140 146 60: 376 type=196 (LJ14) 141 144 60: 377 type=196 (LJ14) 142 144 60: 378 type=196 (LJ14) 143 144 60: 379 type=196 (LJ14) 144 149 60: 380 type=197 (LJ14) 144 150 60: 381 type=198 (LJ14) 144 154 60: 382 type=190 (LJ14) 145 147 60: 383 type=195 (LJ14) 145 148 60: 384 type=186 (LJ14) 146 151 60: 385 type=186 (LJ14) 146 152 60: 386 type=186 (LJ14) 146 153 60: 387 type=188 (LJ14) 146 155 60: 388 type=190 (LJ14) 147 149 60: 389 type=190 (LJ14) 147 150 60: 390 type=190 (LJ14) 147 154 60: 391 type=193 (LJ14) 149 151 60: 392 type=193 (LJ14) 149 152 60: 393 type=193 (LJ14) 149 153 60: 394 type=194 (LJ14) 149 155 60: 395 type=195 (LJ14) 150 155 60: 396 type=196 (LJ14) 151 154 60: 397 type=196 (LJ14) 152 154 60: 398 type=196 (LJ14) 153 154 60: Coulomb-14: 60: nr: 0 60: LJC-14 q: 60: nr: 0 60: LJC Pairs NB: 60: nr: 0 60: LJ (SR): 60: nr: 0 60: Buck.ham (SR): 60: nr: 0 60: LJ: 60: nr: 0 60: B.ham: 60: nr: 0 60: Disper. corr.: 60: nr: 0 60: Coulomb (SR): 60: nr: 0 60: Coul: 60: nr: 0 60: RF excl.: 60: nr: 0 60: Coul. recip.: 60: nr: 0 60: LJ recip.: 60: nr: 0 60: DPD: 60: nr: 0 60: Polarization: 60: nr: 0 60: Water Pol.: 60: nr: 0 60: Thole Pol.: 60: nr: 0 60: Anharm. Pol.: 60: nr: 0 60: Position Rest.: 60: nr: 0 60: Flat-b. P-R.: 60: nr: 0 60: Dis. Rest.: 60: nr: 0 60: D.R.Viol. (nm): 60: nr: 0 60: Orient. Rest.: 60: nr: 0 60: Ori. R. RMSD: 60: nr: 0 60: Angle Rest.: 60: nr: 0 60: Angle Rest. Z: 60: nr: 0 60: Dih. Rest.: 60: nr: 0 60: Dih. Rest. Vi.: 60: nr: 0 60: Constraint: 60: nr: 0 60: Constr. No Co.: 60: nr: 0 60: Settle: 60: nr: 0 60: Virtual site 1: 60: nr: 0 60: Virtual site 2: 60: nr: 0 60: Virt. site 2fd: 60: nr: 0 60: Virtual site 3: 60: nr: 0 60: Virt. site 3fd: 60: nr: 0 60: Vir. site 3fad: 60: nr: 0 60: Vir. site 3out: 60: nr: 0 60: Virt. site 4fd: 60: nr: 0 60: Vir. site 4fdn: 60: nr: 0 60: Virtual site N: 60: nr: 0 60: COM Pull En.: 60: nr: 0 60: Dens. fitting: 60: nr: 0 60: Quantum En.: 60: nr: 0 60: Potential: 60: nr: 0 60: Kinetic En.: 60: nr: 0 60: Total Energy: 60: nr: 0 60: Conserved En.: 60: nr: 0 60: Temperature: 60: nr: 0 60: Vir. Temp.: 60: nr: 0 60: Pres. DC: 60: nr: 0 60: Pressure: 60: nr: 0 60: dH/dl constr.: 60: nr: 0 60: dVremain/dl: 60: nr: 0 60: dEkin/dl: 60: nr: 0 60: dVcoul/dl: 60: nr: 0 60: dVvdw/dl: 60: nr: 0 60: dVbonded/dl: 60: nr: 0 60: dVrestraint/dl: 60: nr: 0 60: dVtemp/dl: 60: nr: 0 60: grp[T-Coupling ] nr=1, name=[ rest] 60: grp[Energy Mon. ] nr=1, name=[ rest] 60: grp[Acc. not used] nr=1, name=[ rest] 60: grp[Freeze ] nr=1, name=[ rest] 60: grp[User1 ] nr=1, name=[ rest] 60: grp[User2 ] nr=1, name=[ rest] 60: grp[VCM ] nr=1, name=[ rest] 60: grp[Compressed X] nr=1, name=[ rest] 60: grp[Or. Res. Fit] nr=1, name=[ rest] 60: grp[QMMM ] nr=1, name=[ rest] 60: grpname (11): 60: grpname[0]={name="System"} 60: grpname[1]={name="Protein"} 60: grpname[2]={name="Protein-H"} 60: grpname[3]={name="C-alpha"} 60: grpname[4]={name="Backbone"} 60: grpname[5]={name="MainChain"} 60: grpname[6]={name="MainChain+Cb"} 60: grpname[7]={name="MainChain+H"} 60: grpname[8]={name="SideChain"} 60: grpname[9]={name="SideChain-H"} 60: grpname[10]={name="rest"} 60: groups T-Cou Energ Acc. Freez User1 User2 VCM Compr Or. R QMMM 60: allocated 0 0 0 0 0 0 0 0 0 0 60: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0 60: box (3x3): 60: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00} 60: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00} 60: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00} 60: box_rel (3x3): 60: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv (3x3): 60: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev (3x3): 60: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev (3x3): 60: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev (3x3): 60: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: nosehoover_xi: not available 60: x (156x3): 60: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00} 60: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00} 60: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00} 60: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00} 60: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00} 60: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00} 60: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00} 60: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00} 60: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01} 60: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01} 60: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01} 60: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00} 60: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01} 60: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01} 60: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01} 60: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01} 60: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01} 60: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01} 60: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01} 60: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01} 60: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01} 60: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01} 60: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00} 60: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00} 60: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00} 60: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00} 60: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00} 60: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01} 60: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00} 60: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00} 60: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00} 60: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00} 60: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01} 60: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01} 60: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00} 60: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00} 60: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00} 60: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00} 60: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01} 60: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01} 60: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01} 60: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01} 60: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01} 60: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01} 60: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01} 60: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01} 60: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01} 60: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01} 60: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01} 60: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01} 60: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01} 60: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01} 60: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01} 60: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01} 60: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01} 60: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01} 60: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01} 60: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01} 60: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01} 60: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01} 60: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01} 60: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01} 60: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01} 60: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01} 60: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01} 60: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01} 60: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01} 60: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01} 60: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01} 60: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01} 60: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01} 60: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01} 60: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01} 60: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01} 60: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02} 60: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02} 60: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02} 60: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02} 60: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02} 60: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01} 60: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02} 60: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01} 60: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02} 60: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01} 60: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01} 60: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01} 60: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02} 60: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01} 60: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02} 60: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01} 60: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02} 60: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01} 60: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01} 60: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02} 60: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02} 60: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02} 60: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01} 60: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02} 60: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02} 60: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02} 60: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02} 60: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02} 60: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01} 60: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01} 60: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01} 60: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01} 60: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01} 60: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01} 60: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01} 60: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01} 60: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01} 60: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01} 60: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01} 60: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01} 60: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01} 60: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01} 60: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01} 60: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01} 60: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01} 60: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01} 60: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01} 60: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01} 60: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01} 60: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01} 60: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01} 60: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02} 60: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01} 60: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01} 60: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01} 60: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01} 60: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01} 60: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01} 60: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01} 60: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01} 60: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02} 60: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02} 60: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02} 60: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02} 60: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01} 60: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01} 60: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01} 60: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01} 60: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01} 60: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01} 60: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01} 60: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01} 60: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01} 60: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01} 60: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01} 60: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01} 60: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01} 60: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01} 60: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01} 60: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02} 60: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01} 60: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01} 60: v (156x3): 60: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} 60: Group statistics 60: T-Coupling : 156 (total 156 atoms) 60: Energy Mon. : 156 (total 156 atoms) 60: Acc. not used: 156 (total 156 atoms) 60: Freeze : 156 (total 156 atoms) 60: User1 : 156 (total 156 atoms) 60: User2 : 156 (total 156 atoms) 60: VCM : 156 (total 156 atoms) 60: Compressed X: 156 (total 156 atoms) 60: Or. Res. Fit: 156 (total 156 atoms) 60: QMMM : 156 (total 156 atoms) 60: [ OK ] DumpTest.WorksWithTpr (44 ms) 60: [ RUN ] DumpTest.WorksWithTprAndMdpWriting 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: [ OK ] DumpTest.WorksWithTprAndMdpWriting (0 ms) 60: [----------] 2 tests from DumpTest (61 ms total) 60: 60: [----------] 3 tests from HelpwritingTest 60: [ RUN ] HelpwritingTest.ConvertTprWritesHelp 60: [ OK ] HelpwritingTest.ConvertTprWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.DumpWritesHelp 60: [ OK ] HelpwritingTest.DumpWritesHelp (0 ms) 60: [ RUN ] HelpwritingTest.ReportMethodsWritesHelp 60: [ OK ] HelpwritingTest.ReportMethodsWritesHelp (0 ms) 60: [----------] 3 tests from HelpwritingTest (0 ms total) 60: 60: [----------] 7 tests from GmxMakeNdx 60: [ RUN ] GmxMakeNdx.WritesDefaultProteinIndexGroups 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 16 Protein residues 60: Analysing Protein... 60: 60: 0 System : 256 atoms 60: 1 Protein : 256 atoms 60: 2 Protein-H : 139 atoms 60: 3 C-alpha : 16 atoms 60: 4 Backbone : 48 atoms 60: 5 MainChain : 63 atoms 60: 6 MainChain+Cb : 78 atoms 60: 7 MainChain+H : 81 atoms 60: 8 SideChain : 175 atoms 60: 9 SideChain-H : 76 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.WritesDefaultProteinIndexGroups (5 ms) 60: [ RUN ] GmxMakeNdx.HandlesNoStructureInput 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 1 'Protein' 60: Copied index group 2 'Protein-H' 60: Merged two groups with OR: 22 10 -> 22 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNoStructureInput (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesNotProtein 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesNotProtein (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexResult 60: Going to read 1 old index file(s) 60: Deducing 22 atoms in the system from indices in the index file 60: 60: 0 System : 22 atoms 60: 1 Protein : 22 atoms 60: 2 Protein-H : 10 atoms 60: 3 C-alpha : 1 atoms 60: 4 Backbone : 5 atoms 60: 5 MainChain : 7 atoms 60: 6 MainChain+Cb : 8 atoms 60: 7 MainChain+H : 9 atoms 60: 8 SideChain : 13 atoms 60: 9 SideChain-H : 3 atoms 60: 10 CA : 1 atoms 60: 11 C_&_r_1 : 1 atoms 60: 12 C_&_r_2 : 1 atoms 60: 13 N_&_r_2 : 1 atoms 60: 14 N_&_r_3 : 1 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Copied index group 4 'Backbone' 60: Copied index group 8 'SideChain' 60: Merged two groups with AND: 5 13 -> 0 60: Group is empty 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexResult (0 ms) 60: [ RUN ] GmxMakeNdx.HandlesEmptyIndexFile 60: Going to read 1 old index file(s) 60: Deducing 6 atoms in the system from indices in the index file 60: 60: 0 System : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Removed group 0 'System' 60: 60: > 60: [ OK ] GmxMakeNdx.HandlesEmptyIndexFile (0 ms) 60: [ RUN ] GmxMakeNdx.Splitres 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into residues 60: 60: > 60: [ OK ] GmxMakeNdx.Splitres (0 ms) 60: [ RUN ] GmxMakeNdx.Splitat 60: 60: Reading structure file 60: Going to read 0 old index file(s) 60: Analysing residue names: 60: There are: 2 Water residues 60: 60: 0 System : 6 atoms 60: 1 Water : 6 atoms 60: 2 SOL : 6 atoms 60: 60: nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 60: 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 60: 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 60: 'r': residue 'res' nr 'chain' char 60: "name": group 'case': case sensitive 'q': save and quit 60: 'ri': residue index 60: 60: > 60: Splitting group 1 'Water' into atoms 60: 60: > 60: [ OK ] GmxMakeNdx.Splitat (0 ms) 60: [----------] 7 tests from GmxMakeNdx (9 ms total) 60: 60: [----------] 4 tests from ReportMethodsTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Setting the LD random seed to -526339 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 60: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 60: [ RUN ] ReportMethodsTest.WritesCorrectInformation 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: [ OK ] ReportMethodsTest.WritesCorrectInformation (0 ms) 60: [ RUN ] ReportMethodsTest.ToolEndToEndTest 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: section: Methods 60: subsection: Simulation system 60: A system of 1 molecules (156 atoms) was simulated. 60: 60: subsection: Simulation settings 60: A total of 0 ns were simulated with a time step of 1 fs. 60: Neighbor searching was performed every 10 steps. 60: The Cut-off algorithm was used for electrostatic interactions. 60: with a cut-off of 1 nm. 60: A single cut-off of 1.1 nm was used for Van der Waals interactions. 60: [ OK ] ReportMethodsTest.ToolEndToEndTest (0 ms) 60: [----------] 4 tests from ReportMethodsTest (0 ms total) 60: 60: [----------] 4 tests from ConvertTprTest 60: [ RUN ] ConvertTprTest.ExtendRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_ExtendRuntimeExtensionTest_extended_again.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting the LD random seed to -168838161 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: Extending remaining runtime by 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 200000 60: Runtime for the run 200 ps 60: Run end step 200000 60: Run end time 200 ps 60: 60: [ OK ] ConvertTprTest.ExtendRuntimeExtensionTest (871 ms) 60: [ RUN ] ConvertTprTest.UntilRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_UntilRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting the LD random seed to 1946122239 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: Extending remaining runtime to 100 ps 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 100000 60: Runtime for the run 100 ps 60: Run end step 100000 60: Run end time 100 ps 60: 60: [ OK ] ConvertTprTest.UntilRuntimeExtensionTest (716 ms) 60: [ RUN ] ConvertTprTest.nstepRuntimeExtensionTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting nsteps to 102 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_nstepRuntimeExtensionTest_extended.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting the LD random seed to -10014756 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: Input file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 0 60: Runtime for the run 0 ps 60: Run end step 0 60: Run end time 0 ps 60: 60: 60: Output file: 60: Run start step 0 60: Run start time 0 ps 60: Step to be made during run 102 60: Runtime for the run 0.102 ps 60: Run end step 102 60: Run end time 0.102 ps 60: 60: [ OK ] ConvertTprTest.nstepRuntimeExtensionTest (674 ms) 60: [ RUN ] ConvertTprTest.generateVelocitiesTest 60: 60: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: For a correct single-point energy evaluation with nsteps = 0, use 60: continuation = yes to avoid constraining the input coordinates. 60: 60: Generating 1-4 interactions: fudge = 0.5 60: 60: NOTE 2 [file lysozyme.top, line 1465]: 60: System has non-zero total charge: 2.000000 60: Total charge should normally be an integer. See 60: https://manual.gromacs.org/current/user-guide/floating-point.html 60: for discussion on how close it should be to an integer. 60: 60: 60: 60: Number of degrees of freedom in T-Coupling group rest is 465.00 60: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 60: 60: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: NVE simulation with an initial temperature of zero: will use a Verlet 60: buffer of 10%. Check your energy drift! 60: 60: 60: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.mdp]: 60: You are using a plain Coulomb cut-off, which might produce artifacts. 60: You might want to consider using PME electrostatics. 60: 60: 60: 60: There were 4 NOTEs 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_lysozyme.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/tools/tests/Testing/Temporary/ConvertTprTest_generateVelocitiesTest_new_velocities.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 60: Setting the LD random seed to -1210352175 60: 60: Generated 330891 of the 330891 non-bonded parameter combinations 60: 60: Generated 330891 of the 330891 1-4 parameter combinations 60: 60: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 60: Analysing residue names: 60: There are: 10 Protein residues 60: Analysing Protein... 60: 60: This run will generate roughly 0 Mb of data 60: [ OK ] ConvertTprTest.generateVelocitiesTest (913 ms) 60: [----------] 4 tests from ConvertTprTest (3176 ms total) 60: 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: trr version: GMX_trn_file (single precision) 60: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_trr (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_tng (20 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_gro (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithIndexGroupSubset/file_spc2_traj_g96 (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_trr (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_tng (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_xtc (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_gro (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_pdb (0 ms) 60: [ RUN ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 60: Will write trr: Trajectory in portable xdr format 60: Group 0 ( System) has 6 elements 60: Group 1 (FirstWaterMolecule) has 3 elements 60: Group 2 (SecondWaterMolecule) has 3 elements 60: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 1.000 -> frame 0 time 0.000 Last frame 1 time 1.000 60: -> frame 1 time 1.000 60: Last written: frame 1 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: Select group for output 60: Selected 2: 'SecondWaterMolecule' 60: [ OK ] Works/TrjconvWithDifferentInputFormats.WithoutTopologyFile/file_spc2_traj_g96 (0 ms) 60: [----------] 12 tests from Works/TrjconvWithDifferentInputFormats (24 ms total) 60: 60: [----------] 30 tests from Works/TrjconvDumpTest 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time__1_00 (24 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_trr_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_tng_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time__1_00 (20 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_xtc_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 Reading frames from gro file 'Generated by trjconv t= 0.00000 step= 0', 6 atoms. 60: Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm) 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_gro_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time__1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frames from pdb file Reading frame 0 time 0.000 Reading frames from pdb file Reading frame 0 time 0.000 60: Precision of /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm) 60: 'Generated by trjconv t= 1.00000 step= 1', 6 atoms 60: Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_pdb_dump_time_999999_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time__1_00 (16 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 0 ps 60: -> frame 0 time 0.000 60: Last written: frame 0 time 0.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_0_30 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_1_00 (0 ms) 60: [ RUN ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 60: Will write trr: Trajectory in portable xdr format 60: Reading frame 0 time 0.000 Reading frame 0 time 0.000 Reading frame 1 time 1.000 Last frame 1 time 1.000 60: 60: Dumping frame at t= 1 ps 60: -> frame 0 time 1.000 60: Last written: frame 0 time 1.000 60: 60: 60: Note that major changes are planned in future for trjconv, to improve usability and utility. 60: [ OK ] Works/TrjconvDumpTest.DumpsFrame/file_spc2_traj_g96_dump_time_999999_00 (0 ms) 60: [----------] 30 tests from Works/TrjconvDumpTest (69 ms total) 60: 60: [----------] Global test environment tear-down 60: [==========] 62 tests from 7 test suites ran. (4944 ms total) 60: [ PASSED ] 62 tests. 60/91 Test #60: ToolUnitTests ................................ Passed 5.15 sec test 61 Start 61: FileIOTests 61: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/fileio-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/FileIOTests.xml" 61: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/fileio/tests 61: Test timeout computed to be: 30 61: [==========] Running 413 tests from 15 test suites. 61: [----------] Global test environment set-up. 61: [----------] 4 tests from Checkpoint 61: [ RUN ] Checkpoint.ReadingThrowsWhenValueNotPresent 61: [ OK ] Checkpoint.ReadingThrowsWhenValueNotPresent (0 ms) 61: [ RUN ] Checkpoint.ReadingDoesNotThrowWhenValuePresent 61: [ OK ] Checkpoint.ReadingDoesNotThrowWhenValuePresent (0 ms) 61: [ RUN ] Checkpoint.KvtRoundTripInt64 61: [ OK ] Checkpoint.KvtRoundTripInt64 (0 ms) 61: [ RUN ] Checkpoint.KvtRoundTripReal 61: [ OK ] Checkpoint.KvtRoundTripReal (0 ms) 61: [----------] 4 tests from Checkpoint (0 ms total) 61: 61: [----------] 1 test from StructureIOTest 61: [ RUN ] StructureIOTest.ReadTpsConfRetainsChainids 61: [ OK ] StructureIOTest.ReadTpsConfRetainsChainids (0 ms) 61: [----------] 1 test from StructureIOTest (0 ms total) 61: 61: [----------] 2 tests from FileMD5Test 61: [ RUN ] FileMD5Test.CanComputeMD5 61: [ OK ] FileMD5Test.CanComputeMD5 (0 ms) 61: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 61: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 61: [----------] 2 tests from FileMD5Test (0 ms total) 61: 61: [----------] 4 tests from FileTypeTest 61: [ RUN ] FileTypeTest.CorrectValueForEmptyString 61: [ OK ] FileTypeTest.CorrectValueForEmptyString (0 ms) 61: [ RUN ] FileTypeTest.CorrectValueForNoExtension 61: [ OK ] FileTypeTest.CorrectValueForNoExtension (0 ms) 61: [ RUN ] FileTypeTest.CorrectValueForEmptyExtension 61: [ OK ] FileTypeTest.CorrectValueForEmptyExtension (0 ms) 61: [ RUN ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters 61: [ OK ] FileTypeTest.CorrectValueForLongExtensionWithStrangeCharacters (0 ms) 61: [----------] 4 tests from FileTypeTest (0 ms total) 61: 61: [----------] 3 tests from MrcSerializer 61: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet 61: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms) 61: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize 61: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms) 61: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip 61: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (0 ms) 61: [----------] 3 tests from MrcSerializer (0 ms total) 61: 61: [----------] 4 tests from MrcDensityMap 61: [ RUN ] MrcDensityMap.RoundTripIsIdempotent 61: [ OK ] MrcDensityMap.RoundTripIsIdempotent (0 ms) 61: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent 61: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms) 61: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile 61: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms) 61: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile 61: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (0 ms) 61: [----------] 4 tests from MrcDensityMap (0 ms total) 61: 61: [----------] 8 tests from MrcDensityMapHeaderTest 61: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader 61: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect 61: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid 61: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven 61: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined 61: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues 61: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents 61: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms) 61: [ RUN ] MrcDensityMapHeaderTest.IsSane 61: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms) 61: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total) 61: 61: [----------] 10 tests from ReadTest 61: [ RUN ] ReadTest.get_eint_ReadsInteger 61: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 61: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 61: 61: ERROR 1 [file unknown]: 61: Right hand side '0.8' for parameter 'test' in parameter file is not an 61: integer value 61: 61: 61: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 61: [ RUN ] ReadTest.get_eint_WarnsAboutString 61: 61: ERROR 1 [file unknown]: 61: Right hand side 'hello' for parameter 'test' in parameter file is not an 61: integer value 61: 61: 61: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 61: [ RUN ] ReadTest.get_eint64_ReadsInteger 61: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 61: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 61: 61: ERROR 1 [file unknown]: 61: Right hand side '0.8' for parameter 'test' in parameter file is not an 61: integer value 61: 61: 61: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 61: [ RUN ] ReadTest.get_eint64_WarnsAboutString 61: 61: ERROR 1 [file unknown]: 61: Right hand side 'hello' for parameter 'test' in parameter file is not an 61: integer value 61: 61: 61: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 61: [ RUN ] ReadTest.get_ereal_ReadsInteger 61: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 61: [ RUN ] ReadTest.get_ereal_ReadsFloat 61: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 61: [ RUN ] ReadTest.get_ereal_WarnsAboutString 61: 61: ERROR 1 [file unknown]: 61: Right hand side 'hello' for parameter 'test' in parameter file is not a 61: real value 61: 61: 61: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 61: [ RUN ] ReadTest.setStringEntry_ReturnsCorrectString 61: [ OK ] ReadTest.setStringEntry_ReturnsCorrectString (0 ms) 61: [----------] 10 tests from ReadTest (0 ms total) 61: 61: [----------] 3 tests from TimeControlTest 61: [ RUN ] TimeControlTest.UnSetHasNoValue 61: [ OK ] TimeControlTest.UnSetHasNoValue (0 ms) 61: [ RUN ] TimeControlTest.CanSetValue 61: [ OK ] TimeControlTest.CanSetValue (0 ms) 61: [ RUN ] TimeControlTest.CanUnsetValueAgain 61: [ OK ] TimeControlTest.CanUnsetValueAgain (0 ms) 61: [----------] 3 tests from TimeControlTest (0 ms total) 61: 61: [----------] 1 test from FileIOXdrSerializerTest 61: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect 61: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms) 61: [----------] 1 test from FileIOXdrSerializerTest (0 ms total) 61: 61: [----------] 1 test from TngTest 61: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 61: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 61: [----------] 1 test from TngTest (0 ms total) 61: 61: [----------] 4 tests from XvgioTest 61: [ RUN ] XvgioTest.readXvgIntWorks 61: [ OK ] XvgioTest.readXvgIntWorks (0 ms) 61: [ RUN ] XvgioTest.readXvgRealWorks 61: [ OK ] XvgioTest.readXvgRealWorks (0 ms) 61: [ RUN ] XvgioTest.readXvgIgnoreCommentLineWorks 61: [ OK ] XvgioTest.readXvgIgnoreCommentLineWorks (0 ms) 61: [ RUN ] XvgioTest.readXvgDeprecatedWorks 61: [ OK ] XvgioTest.readXvgDeprecatedWorks (0 ms) 61: [----------] 4 tests from XvgioTest (0 ms total) 61: 61: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 61: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 61: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 61: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 61: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (0 ms) 61: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 61: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (0 ms) 61: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 61: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 61: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (0 ms total) 61: 61: [----------] 360 tests from FileTypeMatch/FileTypeTest 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/0 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/1 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/2 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/3 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/4 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/5 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/6 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/7 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/8 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/9 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/10 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/11 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/12 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/13 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/14 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/15 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/16 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/17 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/18 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/19 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/20 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/21 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/22 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/23 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/24 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/25 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/26 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/27 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/28 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/29 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/30 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/31 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/32 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/33 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/34 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/35 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/36 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/37 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/38 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/39 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/40 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/41 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/42 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/43 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/44 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/45 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/46 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/47 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/48 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/49 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/50 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/51 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/52 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/53 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/54 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/55 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/56 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/57 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/58 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/59 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/60 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/61 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/62 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/63 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/64 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/65 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/66 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/67 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/68 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/69 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/70 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/71 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/72 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/73 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/74 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/75 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/76 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/77 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/78 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/79 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/80 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/81 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/82 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/83 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/84 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/85 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/86 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/87 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/88 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/89 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/90 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/91 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/92 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/93 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/94 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/95 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/96 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/97 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/98 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/99 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/100 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/101 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/102 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/103 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/104 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/105 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/106 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/107 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/108 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/109 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/110 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/111 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/112 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/113 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/114 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/115 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/116 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/117 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/118 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/119 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/120 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/121 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/122 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/123 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/124 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/125 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/126 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/127 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/128 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/129 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/130 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/131 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/132 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/133 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/134 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/135 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/136 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/137 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/138 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/139 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/140 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/141 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/142 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/143 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/144 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/145 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/146 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/147 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/148 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/149 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/150 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/151 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/152 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/153 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/154 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/155 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/156 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/157 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/158 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/159 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/160 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/161 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/162 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/163 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/164 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/165 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/166 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/167 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/168 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/169 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/170 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/171 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/172 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/173 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/174 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/175 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/176 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/177 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/178 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForNullptr/179 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/0 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/1 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/2 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/3 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/4 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/5 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/6 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/7 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/8 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/9 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/10 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/11 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/12 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/13 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/14 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/15 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/16 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/17 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/18 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/19 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/20 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/21 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/22 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/23 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/24 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/25 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/26 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/27 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/28 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/29 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/30 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/31 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/32 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/33 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/34 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/35 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/36 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/37 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/38 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/39 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/40 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/41 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/42 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/43 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/44 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/45 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/46 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/47 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/48 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/49 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/50 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/51 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/52 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/53 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/54 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/55 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/56 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/57 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/58 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/59 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/60 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/61 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/62 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/63 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/64 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/65 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/66 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/67 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/68 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/69 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/70 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/71 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/72 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/73 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/74 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/75 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/76 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/77 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/78 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/79 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/80 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/81 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/82 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/83 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/84 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/85 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/86 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/87 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/88 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/89 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/90 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/91 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/92 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/93 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/94 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/95 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/96 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/97 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/98 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/99 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/100 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/101 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/102 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/103 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/104 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/105 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/106 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/107 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/108 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/109 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/110 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/111 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/112 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/113 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/114 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/115 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/116 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/117 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/118 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/119 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/120 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/121 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/122 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/123 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/124 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/125 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/126 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/127 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/128 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/129 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/130 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/131 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/132 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/133 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/134 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/135 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/136 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/137 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/138 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/139 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/140 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/141 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/142 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/143 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/144 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/145 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/146 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/147 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/148 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/149 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/150 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/151 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/152 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/153 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/154 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/155 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/156 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/157 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/158 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/159 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/160 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/161 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/162 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/163 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/164 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/165 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/166 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/167 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/168 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/169 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/170 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/171 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/172 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/173 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/174 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/175 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/176 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/177 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/178 (0 ms) 61: [ RUN ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 61: [ OK ] FileTypeMatch/FileTypeTest.CorrectValueForExtension/179 (0 ms) 61: [----------] 360 tests from FileTypeMatch/FileTypeTest (1 ms total) 61: 61: [----------] 4 tests from XvgReadTimeSeries/XvgioTest 61: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 61: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/0 (24 ms) 61: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 61: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/1 (0 ms) 61: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 61: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/2 (0 ms) 61: [ RUN ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 61: [ OK ] XvgReadTimeSeries/XvgioTest.readXvgTimeSeriesWorks/3 (0 ms) 61: [----------] 4 tests from XvgReadTimeSeries/XvgioTest (24 ms total) 61: 61: [----------] Global test environment tear-down 61: [==========] 413 tests from 15 test suites ran. (29 ms total) 61: [ PASSED ] 413 tests. 61/91 Test #61: FileIOTests .................................. Passed 0.27 sec test 62 Start 62: SelectionUnitTests 62: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/selection-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/SelectionUnitTests.xml" 62: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/tests 62: Test timeout computed to be: 30 62: [==========] Running 201 tests from 11 test suites. 62: [----------] Global test environment set-up. 62: [----------] 1 test from IndexGroupTest 62: [ RUN ] IndexGroupTest.RemovesDuplicates 62: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 62: [----------] 1 test from IndexGroupTest (0 ms total) 62: 62: [----------] 15 tests from IndexBlockTest 62: [ RUN ] IndexBlockTest.CreatesUnknownBlock 62: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 62: [ RUN ] IndexBlockTest.CreatesAtomBlock 62: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 62: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology 62: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms) 62: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology 62: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (0 ms) 62: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology 62: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms) 62: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology 62: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms) 62: [ RUN ] IndexBlockTest.CreatesSingleBlock 62: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 62: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 62: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 62: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 62: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 62: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 62: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 62: [----------] 15 tests from IndexBlockTest (0 ms total) 62: 62: [----------] 11 tests from IndexMapTest 62: [ RUN ] IndexMapTest.InitializesAtomBlock 62: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 62: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 62: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 62: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 62: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 62: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 62: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 62: [ RUN ] IndexMapTest.InitializesMoleculeBlock 62: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 62: [ RUN ] IndexMapTest.MapsSingleBlock 62: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 62: [ RUN ] IndexMapTest.MapsResidueBlocks 62: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms) 62: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 62: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 62: [ RUN ] IndexMapTest.HandlesMultipleRequests 62: [ OK ] IndexMapTest.HandlesMultipleRequests (0 ms) 62: [----------] 11 tests from IndexMapTest (1 ms total) 62: 62: [----------] 3 tests from IndexGroupsAndNamesTest 62: [ RUN ] IndexGroupsAndNamesTest.containsNames 62: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms) 62: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing 62: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (12 ms) 62: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect 62: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms) 62: [----------] 3 tests from IndexGroupsAndNamesTest (12 ms total) 62: 62: [----------] 15 tests from NeighborhoodSearchTest 62: [ RUN ] NeighborhoodSearchTest.SimpleSearch 62: [ OK ] NeighborhoodSearchTest.SimpleSearch (35 ms) 62: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 62: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (30 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchBox 62: [ OK ] NeighborhoodSearchTest.GridSearchBox (1 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 62: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (12 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 62: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (2 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 62: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (0 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 62: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (5 ms) 62: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 62: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 62: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (82 ms) 62: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 62: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 62: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 62: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 62: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 62: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 62: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 62: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 62: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 62: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (2 ms) 62: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 62: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (0 ms) 62: [----------] 15 tests from NeighborhoodSearchTest (205 ms total) 62: 62: [----------] 13 tests from PositionCalculationTest 62: [ RUN ] PositionCalculationTest.ComputesAtomPositions 62: [ OK ] PositionCalculationTest.ComputesAtomPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex 62: [ OK ] PositionCalculationTest.ComputesAtomPositionsWithRepeatedIndex (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 62: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 62: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 62: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 62: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 62: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 62: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 62: [ RUN ] PositionCalculationTest.ComputesPositionMask 62: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 62: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 62: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 62: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 62: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 62: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 62: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms) 62: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 62: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 62: [----------] 13 tests from PositionCalculationTest (1 ms total) 62: 62: [----------] 33 tests from SelectionCollectionTest 62: [ RUN ] SelectionCollectionTest.HandlesNoSelections 62: [ OK ] SelectionCollectionTest.HandlesNoSelections (36 ms) 62: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 62: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 62: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 62: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (0 ms) 62: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 62: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 62: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 62: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 62: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 62: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 62: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 62: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 62: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 62: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 62: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 62: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 62: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 62: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 62: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 62: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 62: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (4 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 62: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 62: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 62: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 62: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 62: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 62: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 62: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 62: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 62: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (0 ms) 62: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 62: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (0 ms) 62: [ RUN ] SelectionCollectionTest.RetrieveValidSelection 62: [ OK ] SelectionCollectionTest.RetrieveValidSelection (0 ms) 62: [ RUN ] SelectionCollectionTest.RetrieveInvalidSelection 62: [ OK ] SelectionCollectionTest.RetrieveInvalidSelection (0 ms) 62: [ RUN ] SelectionCollectionTest.CanCopyEmptyCollection 62: [ OK ] SelectionCollectionTest.CanCopyEmptyCollection (0 ms) 62: [ RUN ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately 62: [ OK ] SelectionCollectionTest.CopiedSelectionListsAreHandledSeparately (0 ms) 62: [----------] 33 tests from SelectionCollectionTest (47 ms total) 62: 62: [----------] 14 tests from SelectionCollectionInteractiveTest 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 62: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 62: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 62: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 62: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 62: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (16 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 62: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 62: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 62: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 62: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 62: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 62: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 62: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 62: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 62: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 62: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (14 ms) 62: [----------] 14 tests from SelectionCollectionInteractiveTest (33 ms total) 62: 62: [----------] 70 tests from SelectionCollectionDataTest 62: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 62: [ OK ] SelectionCollectionDataTest.HandlesAllNone (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 62: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesResnr 62: [ OK ] SelectionCollectionDataTest.HandlesResnr (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 62: [ OK ] SelectionCollectionDataTest.HandlesResIndex (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 62: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 62: [ OK ] SelectionCollectionDataTest.HandlesAtomname (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 62: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 62: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesChain 62: [ OK ] SelectionCollectionDataTest.HandlesChain (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesMass 62: [ OK ] SelectionCollectionDataTest.HandlesMass (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesCharge 62: [ OK ] SelectionCollectionDataTest.HandlesCharge (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 62: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 62: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (12 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 62: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBeta 62: [ OK ] SelectionCollectionDataTest.HandlesBeta (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesResname 62: [ OK ] SelectionCollectionDataTest.HandlesResname (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 62: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 62: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 62: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 62: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 62: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 62: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 62: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (16 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 62: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (2 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 62: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (1 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 62: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (9 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 62: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (1 ms) 62: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 62: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (0 ms) 62: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 62: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 62: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (12 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 62: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 62: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 62: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 62: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 62: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 62: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 62: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 62: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (12 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 62: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 62: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 62: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 62: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 62: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 62: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 62: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 62: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 62: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 62: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 62: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (16 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 62: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 62: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 62: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 62: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 62: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 62: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 62: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (16 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 62: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 62: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 62: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 62: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 62: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 62: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 62: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 62: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (0 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 62: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (8 ms) 62: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 62: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (0 ms) 62: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation 62: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPreCompilation (1 ms) 62: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation 62: [ OK ] SelectionCollectionDataTest.CopiedSelectionWorksPostCompilation (1 ms) 62: [ RUN ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent 62: [ OK ] SelectionCollectionDataTest.CopiedSelectionsAreIndependent (17 ms) 62: [ RUN ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation 62: [ OK ] SelectionCollectionDataTest.CopiedSelectionWithIndexPostCompilation (1 ms) 62: [----------] 70 tests from SelectionCollectionDataTest (153 ms total) 62: 62: [----------] 17 tests from SelectionOptionTest 62: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 62: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 62: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 62: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (0 ms) 62: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 62: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 62: [ RUN ] SelectionOptionTest.ChecksEmptySelections 62: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 62: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 62: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooManySelections 62: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 62: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 62: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesAdjuster 62: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 62: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 62: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 62: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 62: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 62: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 62: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 62: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 62: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 62: [----------] 17 tests from SelectionOptionTest (2 ms total) 62: 62: [----------] 9 tests from SelectionFileOptionTest 62: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 62: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 62: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 62: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 62: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 62: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 62: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 62: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 62: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 62: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms) 62: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 62: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 62: [----------] 9 tests from SelectionFileOptionTest (1 ms total) 62: 62: [----------] Global test environment tear-down 62: [==========] 201 tests from 11 test suites ran. (460 ms total) 62: [ PASSED ] 201 tests. 62/91 Test #62: SelectionUnitTests ........................... Passed 0.70 sec test 63 Start 63: MdrunOutputTests 63: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunOutputTests.xml" 63: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 63: Test timeout computed to be: 600 63: [==========] Running 12 tests from 5 test suites. 63: [----------] Global test environment set-up. 63: [----------] 1 test from MdrunTest 63: [ RUN ] MdrunTest.WritesHelp 63: [ OK ] MdrunTest.WritesHelp (26 ms) 63: [----------] 1 test from MdrunTest (26 ms total) 63: 63: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 63: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to -68440418 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 49 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.082 0.041 199.7 63: (ns/day) (hour/ns) 63: Performance: 4.186 5.734 63: Reading frame 0 time 0.000 63: # Atoms 6 63: Reading frame 1 time 0.001 Last frame 1 time 0.001 63: 63: 63: Item #frames Timestep (ps) 63: Step 2 0.001 63: Time 2 0.001 63: Lambda 0 63: Coords 2 0.001 63: Velocities 0 63: Forces 0 63: Box 2 0.001 63: Checking file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 63: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (72 ms) 63: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to 2121086174 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.051 0.025 199.5 63: (ns/day) (hour/ns) 63: Performance: 6.778 3.541 63: Reading frame 0 time 0.000 63: # Atoms 6 63: Reading frame 1 time 0.001 Last frame 1 time 0.001 63: 63: 63: Item #frames Timestep (ps) 63: Step 2 0.001 63: Time 2 0.001 63: Lambda 0 63: Coords 2 0.001 63: Velocities 0 63: Forces 0 63: Box 2 0.001 63: Checking file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 63: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (62 ms) 63: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 63: Generating 1-4 interactions: fudge = 0.5 63: Number of degrees of freedom in T-Coupling group rest is 9.00 63: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 63: NVE simulation: will use the initial temperature of 2573.591 K for 63: determining the Verlet buffer size 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There were 2 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc2' 63: 1 steps, 0.0 ps. 63: Setting the LD random seed to 2146393983 63: 63: Generated 3 of the 3 non-bonded parameter combinations 63: 63: Generated 3 of the 3 1-4 parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.153 nm, buffer size 0.153 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.127 nm, buffer size 0.127 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.047 0.024 199.5 63: (ns/day) (hour/ns) 63: Performance: 7.298 3.289 63: Reading frame 0 time 0.000 63: # Atoms 3 63: Reading frame 1 time 0.001 Last frame 1 time 0.001 63: 63: 63: Item #frames Timestep (ps) 63: Step 2 0.001 63: Time 2 0.001 63: Lambda 0 63: Coords 2 0.001 63: Velocities 0 63: Forces 0 63: Box 2 0.001 63: Checking file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 63: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (56 ms) 63: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (192 ms total) 63: 63: [----------] 2 tests from Argon12/OutputFiles 63: [ RUN ] Argon12/OutputFiles.FilesArePresent/0 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 15 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.276 0.138 199.9 63: (ns/day) (hour/ns) 63: Performance: 10.645 2.255 63: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (169 ms) 63: [ RUN ] Argon12/OutputFiles.FilesArePresent/1 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 63: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 63: that with the Verlet scheme, nstlist has no effect on the accuracy of 63: your simulation. 63: 63: 63: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 63: Setting nstcalcenergy (100) equal to nstenergy (4) 63: 63: Number of degrees of freedom in T-Coupling group System is 33.00 63: 63: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]: 63: NVE simulation: will use the initial temperature of 68.810 K for 63: determining the Verlet buffer size 63: 63: 63: There were 3 NOTEs 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Can not increase nstlist because an NVE ensemble is used 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'Argon' 63: 16 steps, 0.0 ps. 63: Generated 1 of the 1 non-bonded parameter combinations 63: 63: Excluding 1 bonded neighbours molecule type 'Argon' 63: 63: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 63: 63: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.284 0.142 200.0 63: (ns/day) (hour/ns) 63: Performance: 10.344 2.320 63: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (153 ms) 63: [----------] 2 tests from Argon12/OutputFiles (323 ms total) 63: 63: [----------] 3 tests from MdrunCanWrite/Trajectories 63: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 6 steps, 0.0 ps. 63: Setting the LD random seed to -1074417729 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: NOTE: 22 % of the run time was spent in pair search, 63: you might want to increase nstlist (this has no effect on accuracy) 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.139 0.069 199.9 63: (ns/day) (hour/ns) 63: Performance: 8.727 2.750 63: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (88 ms) 63: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 6 steps, 0.0 ps. 63: Setting the LD random seed to -4201602 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.132 0.066 199.9 63: (ns/day) (hour/ns) 63: Performance: 9.168 2.618 63: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (83 ms) 63: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 6 steps, 0.0 ps. 63: Setting the LD random seed to 1045313484 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.108 0.054 199.8 63: (ns/day) (hour/ns) 63: Performance: 11.174 2.148 63: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (81 ms) 63: [----------] 3 tests from MdrunCanWrite/Trajectories (254 ms total) 63: 63: [----------] 3 tests from MdrunCanWrite/NptTrajectories 63: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -419433665 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.011 0.006 198.1 63: (ns/day) (hour/ns) 63: Performance: 46.094 0.521 63: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (17 ms) 63: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 63: 63: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 63: The Berendsen barostat does not generate any strictly correct ensemble, 63: and should not be used for new production simulations (in our opinion). 63: We recommend using the C-rescale barostat instead. 63: 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: 63: There was 1 WARNING 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to 1995323385 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.085 0.043 199.7 63: (ns/day) (hour/ns) 63: Performance: 6.054 3.964 63: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (78 ms) 63: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 63: Number of degrees of freedom in T-Coupling group System is 12.00 63: 63: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 63: You are using a plain Coulomb cut-off, which might produce artifacts. 63: You might want to consider using PME electrostatics. 63: 63: 63: 63: There was 1 NOTE 63: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 63: Changing nstlist from 10 to 40, rlist from 1.031 to 1.172 63: 63: Using 1 MPI process 63: Using 2 OpenMP threads 63: 63: 63: NOTE: The number of threads is not equal to the number of (logical) cpus 63: and the -pin option is set to auto: will not pin threads to cpus. 63: This can lead to significant performance degradation. 63: Consider using -pin on (and -pinoffset in case you run multiple jobs). 63: starting mdrun 'spc-and-methanol' 63: 2 steps, 0.0 ps. 63: Setting the LD random seed to -1116255059 63: 63: Generated 8 of the 10 non-bonded parameter combinations 63: 63: Excluding 2 bonded neighbours molecule type 'Methanol' 63: 63: Excluding 2 bonded neighbours molecule type 'SOL' 63: 63: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 63: 63: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 63: 63: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 63: 63: Note that mdrun will redetermine rlist based on the actual pair-list setup 63: 63: This run will generate roughly 0 Mb of data 63: 63: Writing final coordinates. 63: 63: Core t (s) Wall t (s) (%) 63: Time: 0.093 0.046 199.7 63: (ns/day) (hour/ns) 63: Performance: 5.577 4.303 63: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (75 ms) 63: [----------] 3 tests from MdrunCanWrite/NptTrajectories (171 ms total) 63: 63: [----------] Global test environment tear-down 63: [==========] 12 tests from 5 test suites ran. (1013 ms total) 63: [ PASSED ] 12 tests. 63/91 Test #63: MdrunOutputTests ............................. Passed 1.16 sec test 64 Start 64: MdrunModulesTests 64: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunModulesTests.xml" 64: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 64: Test timeout computed to be: 600 64: [==========] Running 15 tests from 3 test suites. 64: [----------] Global test environment set-up. 64: [----------] 9 tests from DensityFittingTest 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = -3.8565254e+03 64: Maximum force = 4.5099883e+03 on atom 3 64: Norm of force = 1.6816849e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -56802325 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (70 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = -9.8207725e+03 64: Maximum force = 7.3954834e+03 on atom 2 64: Norm of force = 2.7825089e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslation.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -67174601 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslation (23 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyTranslationParametersOff (0 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Overriding nsteps with value passed on the command line: 4 steps 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 4 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 5 steps. 64: Potential Energy = -1.0954996e+04 64: Maximum force = 7.4724795e+03 on atom 2 64: Norm of force = 2.7758003e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 Setting the LD random seed to -270811137 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductTranslationAndTransformationMatrix (45 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyMatrixTransfromationOff (0 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = -3.8565254e+03 64: Maximum force = 4.5099883e+03 on atom 3 64: Norm of force = 1.6816849e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -674758658 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProductIdentityMatrix (35 ms) 64: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = -2.7138664e+04 64: Maximum force = 6.7827656e+03 on atom 2 64: Norm of force = 1.9608866e+03 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Last energy frame read 2 time 2.000 Setting the LD random seed to -2121737 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (31 ms) 64: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch 64: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (0 ms) 64: [ RUN ] DensityFittingTest.CheckpointWorks 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 64: Setting nstcalcenergy (100) equal to nstenergy (2) 64: 64: Number of degrees of freedom in T-Coupling group rest is 33.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]: 64: NVE simulation: will use the initial temperature of 68.810 K for 64: determining the Verlet buffer size 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -306315275 64: 64: Generated 1 of the 1 non-bonded parameter combinations 64: 64: Excluding 1 bonded neighbours molecule type 'Argon' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.052 0.026 199.7 64: (ns/day) (hour/ns) 64: Performance: 9.931 2.417 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps 64: Can not increase nstlist because an NVE ensemble is used 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting mdrun 'Argon' 64: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps). 64: 64: Writing final coordinates. 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.066 0.033 199.7 64: (ns/day) (hour/ns) 64: Performance: 13.021 1.843 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.002 Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (86 ms) 64: [----------] 9 tests from DensityFittingTest (293 ms total) 64: 64: [----------] 4 tests from MimicTest 64: [ RUN ] MimicTest.OneQuantumMol 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 21.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 64: 64: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 83 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.023 0.012 199.4 64: (ns/day) (hour/ns) 64: Performance: 7.492 3.203 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -75570183 64: 64: Generated 10 of the 10 non-bonded parameter combinations 64: 64: Generated 10 of the 10 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MimicTest.OneQuantumMol (17 ms) 64: [ RUN ] MimicTest.AllQuantumMol 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 21.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 64: 64: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 15 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.023 0.012 199.5 64: (ns/day) (hour/ns) 64: Performance: 7.341 3.270 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -1343230049 64: 64: Generated 10 of the 10 non-bonded parameter combinations 64: 64: Generated 10 of the 10 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MimicTest.AllQuantumMol (17 ms) 64: [ RUN ] MimicTest.TwoQuantumMol 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 21.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 64: NVE simulation with an initial temperature of zero: will use a Verlet 64: buffer of 10%. Check your energy drift! 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 64: 64: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: NOTE: 46 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.007 0.004 197.7 64: (ns/day) (hour/ns) 64: Performance: 23.454 1.023 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to -33572100 64: 64: Generated 10 of the 10 non-bonded parameter combinations 64: 64: Generated 10 of the 10 1-4 parameter combinations 64: 64: Excluding 2 bonded neighbours molecule type 'SOL' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MimicTest.TwoQuantumMol (16 ms) 64: [ RUN ] MimicTest.BondCuts 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 64: For a correct single-point energy evaluation with nsteps = 0, use 64: continuation = yes to avoid constraining the input coordinates. 64: 64: Generating 1-4 interactions: fudge = 0.5 64: Number of degrees of freedom in T-Coupling group rest is 66.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 64: NVE simulation: will use the initial temperature of 300.368 K for 64: determining the Verlet buffer size 64: 64: 64: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 3 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Can not increase nstlist because an NVE ensemble is used 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 64: 64: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 64: Reading frame 0 time 0.000 Last frame 0 time 0.000 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.036 0.018 199.6 64: (ns/day) (hour/ns) 64: Performance: 4.797 5.003 64: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 64: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Setting the LD random seed to 2146887479 64: 64: Generated 2211 of the 2211 non-bonded parameter combinations 64: 64: Generated 2211 of the 2211 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] MimicTest.BondCuts (49 ms) 64: [----------] 4 tests from MimicTest (100 ms total) 64: 64: [----------] 2 tests from WithIntegrator/ImdTest 64: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0 64: Generating 1-4 interactions: fudge = 1 64: 64: NOTE 1 [file glycine_vacuo.top, line 12]: 64: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an 64: estimated oscillational period of 1.0e-02 ps, which is less than 10 times 64: the time step of 2.0e-03 ps. 64: Maybe you forgot to change the constraints mdp option. 64: 64: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Changing nstlist from 10 to 25, rlist from 1.071 to 1.232 64: 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: IMD: Enabled. This simulation will accept incoming IMD connections. 64: IMD: Pulling from IMD remote is enabled (-imdpull). 64: IMD: Setting port for connection requests to 0. 64: IMD: Setting up incoming socket. 64: IMD: Listening for IMD connection on port 44033. 64: IMD: -imdwait not set, starting simulation. 64: starting mdrun 'Glycine' 64: 2 steps, 0.0 ps. 64: Setting the LD random seed to -595865880 64: 64: Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 64: 64: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 64: 64: Set rlist, assuming 4x4 atom pair-list, to 1.071 nm, buffer size 0.071 nm 64: 64: Note that mdrun will redetermine rlist based on the actual pair-list setup 64: 64: This run will generate roughly 0 Mb of data 64: 64: Writing final coordinates. 64: 64: NOTE: 29 % of the run time was spent in pair search, 64: you might want to increase nstlist (this has no effect on accuracy) 64: 64: Core t (s) Wall t (s) (%) 64: Time: 0.081 0.041 199.7 64: (ns/day) (hour/ns) 64: Performance: 12.767 1.880 64: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (207 ms) 64: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1 64: 64: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 64: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not 64: apply to steep. 64: 64: Generating 1-4 interactions: fudge = 1 64: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD). 64: Number of degrees of freedom in T-Coupling group System is 27.00 64: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 64: 64: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]: 64: You are using a plain Coulomb cut-off, which might produce artifacts. 64: You might want to consider using PME electrostatics. 64: 64: 64: 64: There were 2 NOTEs 64: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 64: Using 1 MPI process 64: Using 2 OpenMP threads 64: 64: 64: NOTE: The number of threads is not equal to the number of (logical) cpus 64: and the -pin option is set to auto: will not pin threads to cpus. 64: This can lead to significant performance degradation. 64: Consider using -pin on (and -pinoffset in case you run multiple jobs). 64: 64: IMD: Enabled. This simulation will accept incoming IMD connections. 64: IMD: Pulling from IMD remote is enabled (-imdpull). 64: IMD: Setting port for connection requests to 0. 64: IMD: Setting up incoming socket. 64: IMD: Listening for IMD connection on port 49877. 64: IMD: -imdwait not set, starting simulation. 64: 64: Steepest Descents: 64: Tolerance (Fmax) = 1.00000e+01 64: Number of steps = 2 64: 64: Energy minimization reached the maximum number of steps before the forces 64: reached the requested precision Fmax < 10. 64: 64: writing lowest energy coordinates. 64: 64: Steepest Descents did not converge to Fmax < 10 in 3 steps. 64: Potential Energy = 1.1977061e+03 64: Maximum force = 1.7794875e+04 on atom 9 64: Norm of force = 7.8732895e+03 64: Setting the LD random seed to -108203531 64: 64: Generated 20503 of the 20503 non-bonded parameter combinations 64: 64: Generated 17396 of the 20503 1-4 parameter combinations 64: 64: Excluding 3 bonded neighbours molecule type 'Glycine' 64: 64: This run will generate roughly 0 Mb of data 64: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (226 ms) 64: [----------] 2 tests from WithIntegrator/ImdTest (433 ms total) 64: 64: [----------] Global test environment tear-down 64: [==========] 15 tests from 3 test suites ran. (852 ms total) 64: [ PASSED ] 15 tests. 64/91 Test #64: MdrunModulesTests ............................ Passed 1.01 sec test 65 Start 65: MdrunIOTests 65: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunIOTests.xml" 65: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 65: Test timeout computed to be: 600 65: [==========] Running 76 tests from 13 test suites. 65: [----------] Global test environment set-up. 65: [----------] 9 tests from GromppTest 65: [ RUN ] GromppTest.EmptyMdpFileWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Number of degrees of freedom in T-Coupling group rest is 12.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Setting the LD random seed to -906364964 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.EmptyMdpFileWorks (11 ms) 65: [ RUN ] GromppTest.SimulatedAnnealingWorks 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Simulated annealing for group rest: Periodic, 4 timepoints 65: Time (ps) Temperature (K) 65: 0.0 298.0 65: 2.0 320.0 65: 4.0 320.0 65: 6.0 298.0 65: Number of degrees of freedom in T-Coupling group rest is 12.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Setting the LD random seed to 1555001340 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.SimulatedAnnealingWorks (6 ms) 65: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Simulated annealing for group Methanol: Single, 3 timepoints 65: Time (ps) Temperature (K) 65: 0.0 298.0 65: 3.0 280.0 65: 6.0- 270.0 65: Simulated annealing for group SOL: Periodic, 4 timepoints 65: Time (ps) Temperature (K) 65: 0.0 298.0 65: 2.0 320.0 65: 4.0 320.0 65: 6.0 298.0 65: Number of degrees of freedom in T-Coupling group Methanol is 7.20 65: Number of degrees of freedom in T-Coupling group SOL is 4.80 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Setting the LD random seed to -208668865 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (6 ms) 65: [ RUN ] GromppTest.DeathTestHandlesNoMaxwarnError 65: [ OK ] GromppTest.DeathTestHandlesNoMaxwarnError (0 ms) 65: [ RUN ] GromppTest.HandlesMaxwarn 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: 65: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 65: The Berendsen thermostat does not generate the correct kinetic energy 65: distribution, and should not be used for new production simulations (in 65: our opinion). We would recommend the V-rescale thermostat. 65: 65: Number of degrees of freedom in T-Coupling group System is 12.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_HandlesMaxwarn_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: 65: There was 1 WARNING 65: Setting the LD random seed to 1543437243 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.040 nm, buffer size 0.040 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.031 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.HandlesMaxwarn (2 ms) 65: [ RUN ] GromppTest.MaxwarnShouldBePositive 65: [ OK ] GromppTest.MaxwarnShouldBePositive (5 ms) 65: [ RUN ] GromppTest.ValidTransformationCoord 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Pull group 1 'SOL' has 3 atoms 65: Pull group 2 'Methanol' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 12.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_ValidTransformationCoord_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 5 65: 2 3 2 0.613 nm 0.000 nm 65: 1 3 5 65: 2 3 2 0.613 nm 0.000 nm 65: 65: There were 3 NOTEs 65: Setting the LD random seed to -67916171 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: [ OK ] GromppTest.ValidTransformationCoord (7 ms) 65: [ RUN ] GromppTest.InvalidTransformationCoord 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 65: For a correct single-point energy evaluation with nsteps = 0, use 65: continuation = yes to avoid constraining the input coordinates. 65: 65: Pull group 1 'SOL' has 3 atoms 65: Pull group 2 'Methanol' has 3 atoms 65: Number of degrees of freedom in T-Coupling group rest is 12.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 65: NVE simulation: will use the initial temperature of 1046.791 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/GromppTest_InvalidTransformationCoord_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 5 65: 2 3 2 0.613 nm 0.000 nm 65: 1 3 5 65: 2 3 2 Setting the LD random seed to -8979457 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.089 nm, buffer size 0.089 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.072 nm, buffer size 0.072 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: [ OK ] GromppTest.InvalidTransformationCoord (7 ms) 65: [ RUN ] GromppTest.RejectCRescaleAndAnisotropic 65: [ OK ] GromppTest.RejectCRescaleAndAnisotropic (0 ms) 65: [----------] 9 tests from GromppTest (49 ms total) 65: 65: [----------] 6 tests from MdrunTerminationTest 65: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -278200390 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.044 0.022 199.5 65: (ns/day) (hour/ns) 65: Performance: 11.749 2.043 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.036 0.018 199.5 65: (ns/day) (hour/ns) 65: Performance: 14.350 1.673 65: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (66 ms) 65: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 1, rlist from 1.032 to 1 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 100 steps, 0.1 ps. 65: 65: Step 0: Run time exceeded 0.000 hours, will terminate the run within 200 steps 65: Setting the LD random seed to -539115617 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: NOTE: 38 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.039 0.020 199.4 65: (ns/day) (hour/ns) 65: Performance: 8.754 2.742 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 102 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 102 steps, 0.1 ps (continuing from step 1, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 100 65: Runtime for the run 0.1 ps 65: Run end step 100 65: Run end time 0.1 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 102 65: Runtime for the run 0.102 ps 65: Run end step 102 65: Run end time 0.102 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.125 0.562 200.0 65: (ns/day) (hour/ns) 65: Performance: 15.668 1.532 65: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (603 ms) 65: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -1610946114 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.038 0.019 199.4 65: (ns/day) (hour/ns) 65: Performance: 13.540 1.772 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Writing final coordinates. 65: 65: NOTE: 10 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.037 0.018 199.5 65: (ns/day) (hour/ns) 65: Performance: 14.131 1.698 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 6 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 6 65: Runtime for the run 0.006 ps 65: Run end step 6 65: Run end time 0.006 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.037 0.019 199.5 65: (ns/day) (hour/ns) 65: Performance: 14.000 1.714 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 8 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 6 65: Runtime for the run 0.006 ps 65: Run end step 6 65: Run end time 0.006 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 8 65: Runtime for the run 0.008 ps 65: Run end step 8 65: Run end time 0.008 ps 65: 65: 65: Writing final coordinates. 65: 65: NOTE: 30 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.040 0.020 199.5 65: (ns/day) (hour/ns) 65: Performance: 13.029 1.842 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: NOTE: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.023 0.011 199.2 65: (ns/day) (hour/ns) 65: Performance: 7.577 3.167 65: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (154 ms) 65: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to 1930932173 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.109 0.055 199.7 65: (ns/day) (hour/ns) 65: Performance: 4.741 5.062 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps. 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Writing final coordinates. 65: 65: NOTE: 20 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.139 0.069 199.8 65: (ns/day) (hour/ns) 65: Performance: 6.221 3.858 65: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (160 ms) 65: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to 2113400541 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 23 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.095 0.048 199.7 65: (ns/day) (hour/ns) 65: Performance: 5.446 4.407 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (68 ms) 65: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There was 1 NOTE 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 2 steps, 0.0 ps. 65: Setting the LD random seed to -318780426 65: 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.032 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 25 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.102 0.051 199.8 65: (ns/day) (hour/ns) 65: Performance: 5.097 4.709 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Setting nsteps to 4 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 10 to 50, rlist from 1.032 to 1.21 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 65: Input file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 2 65: Runtime for the run 0.002 ps 65: Run end step 2 65: Run end time 0.002 ps 65: 65: 65: Output file: 65: Run start step 0 65: Run start time 0 ps 65: Step to be made during run 4 65: Runtime for the run 0.004 ps 65: Run end step 4 65: Run end time 0.004 ps 65: 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.074 0.037 199.8 65: (ns/day) (hour/ns) 65: Performance: 6.993 3.432 65: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (125 ms) 65: [----------] 6 tests from MdrunTerminationTest (1178 ms total) 65: 65: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks 65: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.369 0.184 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.967 3.013 65: trr version: GMX_trn_file (single precision) 65: 65: 65: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/0 (250 ms) 65: [ RUN ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CheckpointCoordinatesAreSane_CheckpointCoordinatesSanityChecks_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.535 0.267 200.0 65: (ns/day) (hour/ns) 65: Performance: 5.493 4.370 65: 65: 65: [ OK ] CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks.WithinTolerances/1 (294 ms) 65: [----------] 2 tests from CheckpointCoordinatesAreSane/CheckpointCoordinatesSanityChecks (545 ms total) 65: 65: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.471 0.236 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.233 3.851 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.255 0.128 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.085 3.944 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 11 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.262 0.131 199.9 65: (ns/day) (hour/ns) 65: Performance: 5.927 4.050 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (607 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.387 0.193 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.592 3.161 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.185 0.093 199.9 65: (ns/day) (hour/ns) 65: Performance: 8.387 2.861 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.211 0.105 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.377 3.253 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (453 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.492 0.246 200.0 65: (ns/day) (hour/ns) 65: Performance: 5.968 4.021 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 20 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.310 0.155 200.0 65: (ns/day) (hour/ns) 65: Performance: 5.009 4.791 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.212 0.106 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.315 3.281 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (587 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.425 0.213 200.0 65: (ns/day) (hour/ns) 65: Performance: 6.903 3.477 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 10 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.201 0.100 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.747 3.098 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.240 0.120 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.474 3.707 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (517 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.402 0.201 200.0 65: (ns/day) (hour/ns) 65: Performance: 7.302 3.287 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 11 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.223 0.112 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.964 3.446 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.194 0.097 199.9 65: (ns/day) (hour/ns) 65: Performance: 8.027 2.990 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (466 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.711 nm, buffer size 0.011 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.709 nm, buffer size 0.009 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.378 0.189 200.0 65: (ns/day) (hour/ns) 65: Performance: 7.775 3.087 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.200 0.100 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.777 3.086 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.709 to 0.733 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.176 0.088 199.9 65: (ns/day) (hour/ns) 65: Performance: 8.836 2.716 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (458 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 13 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.365 0.182 199.9 65: (ns/day) (hour/ns) 65: Performance: 8.050 2.981 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 16 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.211 0.106 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.351 3.265 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.226 0.113 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.887 3.485 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (468 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.368 0.184 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.971 3.011 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.222 0.111 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.990 3.433 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.218 0.109 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.125 3.369 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (484 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.450 0.225 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.531 3.675 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.242 0.121 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.418 3.739 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.263 0.132 199.9 65: (ns/day) (hour/ns) 65: Performance: 5.908 4.062 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (562 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.462 0.231 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.351 3.779 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 13 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.315 0.158 199.9 65: (ns/day) (hour/ns) 65: Performance: 4.933 4.865 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.220 0.110 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.057 3.401 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (564 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.906 nm, buffer size 0.206 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.892 nm, buffer size 0.192 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.578 0.289 200.0 65: (ns/day) (hour/ns) 65: Performance: 5.079 4.725 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.279 0.139 199.9 65: (ns/day) (hour/ns) 65: Performance: 5.579 4.302 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.261 0.131 199.9 65: (ns/day) (hour/ns) 65: Performance: 5.956 4.029 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (674 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.886 nm, buffer size 0.186 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.872 nm, buffer size 0.172 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.510 0.255 200.0 65: (ns/day) (hour/ns) 65: Performance: 5.759 4.167 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 13 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.240 0.120 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.470 3.710 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.231 0.116 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.720 3.572 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (544 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.329 0.165 199.9 65: (ns/day) (hour/ns) 65: Performance: 8.924 2.689 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.203 0.101 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.673 3.128 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.190 0.095 199.9 65: (ns/day) (hour/ns) 65: Performance: 8.184 2.932 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_12_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/12 (450 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.730 nm, buffer size 0.030 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.362 0.181 199.9 65: (ns/day) (hour/ns) 65: Performance: 8.101 2.963 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.248 0.124 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.264 3.831 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.73 to 0.811 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.238 0.119 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.523 3.679 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_13_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/13 (492 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.760 nm, buffer size 0.060 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.527 0.264 200.0 65: (ns/day) (hour/ns) 65: Performance: 5.572 4.307 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.255 0.127 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.104 3.932 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.275 0.137 199.9 65: (ns/day) (hour/ns) 65: Performance: 5.657 4.242 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_14_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/14 (627 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.757 nm, buffer size 0.057 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.752 nm, buffer size 0.052 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.484 0.242 200.0 65: (ns/day) (hour/ns) 65: Performance: 6.066 3.956 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.282 0.141 199.9 65: (ns/day) (hour/ns) 65: Performance: 5.521 4.347 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.752 to 0.89 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.320 0.160 199.9 65: (ns/day) (hour/ns) 65: Performance: 4.858 4.940 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_15_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/15 (649 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.118 0.059 199.8 65: (ns/day) (hour/ns) 65: Performance: 24.962 0.961 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.783 0.392 200.0 65: (ns/day) (hour/ns) 65: Performance: 1.985 12.088 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.739 0.370 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.103 11.412 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_16_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/16 (1077 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.146 0.573 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.563 9.363 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.601 0.301 199.9 65: (ns/day) (hour/ns) 65: Performance: 2.587 9.279 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.647 0.324 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.401 9.995 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_17_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/17 (1386 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.362 0.681 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.157 11.127 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.738 0.369 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.105 11.399 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.663 0.332 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.346 10.232 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_18_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/18 (1564 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: NVE simulation: will use the initial temperature of 456.887 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 6 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 456.887 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.338 0.669 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.195 10.934 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.786 0.393 200.0 65: (ns/day) (hour/ns) 65: Performance: 1.979 12.128 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.631 0.316 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.465 9.738 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_19_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/19 (1531 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.374 0.687 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.138 11.224 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.461 0.231 199.9 65: (ns/day) (hour/ns) 65: Performance: 3.370 7.122 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.599 0.300 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.595 9.249 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_20_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/20 (1543 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.747 nm, buffer size 0.047 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.836 0.418 200.0 65: (ns/day) (hour/ns) 65: Performance: 3.513 6.832 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.486 0.243 199.9 65: (ns/day) (hour/ns) 65: Performance: 3.200 7.500 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 80, rlist from 0.741 to 0.841 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.713 0.356 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.181 11.002 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_21_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/21 (1484 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 2.031 1.016 200.0 65: (ns/day) (hour/ns) 65: Performance: 1.446 16.598 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.087 0.543 200.0 65: (ns/day) (hour/ns) 65: Performance: 1.431 16.773 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.767 0.384 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.027 11.840 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_22_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/22 (2287 ms) 65: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: 65: NOTE 3 [file unknown]: 65: You are using constraints on all bonds, whereas the forcefield has been 65: parametrized only with constraints involving hydrogen atoms. We suggest 65: using constraints = h-bonds instead, this will also improve performance. 65: 65: Number of degrees of freedom in T-Coupling group System is 23.00 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: There are 9 non-linear virtual site constructions. Their contribution to 65: the energy error is approximated. In most cases this does not affect the 65: error significantly. 65: 65: 65: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 5 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 65: 65: turning all bonds into constraints... 65: 65: Cleaning up constraints and constant bonded interactions with virtual sites 65: 65: Removed 18 Angles with virtual sites, 21 left 65: 65: Removed 10 Proper Dih.s with virtual sites, 44 left 65: 65: Converted 15 Constraints with virtual sites to connections, 7 left 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.728 nm, buffer size 0.028 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.724 nm, buffer size 0.024 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 1.019 0.510 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.882 8.326 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.636 0.318 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.446 9.811 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 25, rlist from 0.724 to 0.793 65: 65: Update groups can not be used for this system because an incompatible virtual site type is used 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine dipeptide in vacuo' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.523 0.261 200.0 65: (ns/day) (hour/ns) 65: Performance: 2.975 8.067 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_23_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/23 (1336 ms) 65: [----------] 24 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (20825 ms total) 65: 65: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.264 0.132 199.9 65: (ns/day) (hour/ns) 65: Performance: 11.128 2.157 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.137 0.068 199.8 65: (ns/day) (hour/ns) 65: Performance: 11.374 2.110 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.146 0.073 199.8 65: (ns/day) (hour/ns) 65: Performance: 10.624 2.259 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (354 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.268 0.134 199.9 65: (ns/day) (hour/ns) 65: Performance: 10.975 2.187 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.103 0.052 199.7 65: (ns/day) (hour/ns) 65: Performance: 15.051 1.595 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.126 0.063 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.326 1.947 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (310 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.406 0.203 200.0 65: (ns/day) (hour/ns) 65: Performance: 7.230 3.319 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 10 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.195 0.098 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.954 3.017 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.129 0.065 199.7 65: (ns/day) (hour/ns) 65: Performance: 12.044 1.993 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (434 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: NVE simulation: will use the initial temperature of 293.480 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 4 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 293.48 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.235 0.117 199.9 65: (ns/day) (hour/ns) 65: Performance: 12.504 1.919 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.148 0.074 199.9 65: (ns/day) (hour/ns) 65: Performance: 10.499 2.286 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.167 0.083 199.8 65: (ns/day) (hour/ns) 65: Performance: 9.325 2.574 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (307 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.736 nm, buffer size 0.036 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.732 nm, buffer size 0.032 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.190 0.095 199.8 65: (ns/day) (hour/ns) 65: Performance: 15.485 1.550 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.102 0.051 199.7 65: (ns/day) (hour/ns) 65: Performance: 15.172 1.582 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.101 0.051 199.7 65: (ns/day) (hour/ns) 65: Performance: 15.376 1.561 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (251 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.214 0.107 199.9 65: (ns/day) (hour/ns) 65: Performance: 13.716 1.750 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.126 0.063 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.371 1.940 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.728 to 0.806 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.111 0.056 199.7 65: (ns/day) (hour/ns) 65: Performance: 13.979 1.717 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (345 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.258 0.129 199.9 65: (ns/day) (hour/ns) 65: Performance: 11.374 2.110 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.125 0.063 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.437 1.930 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.125 0.063 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.423 1.932 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (303 ms) 65: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.756 nm, buffer size 0.056 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.359 0.179 199.9 65: (ns/day) (hour/ns) 65: Performance: 8.184 2.933 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.167 0.092 182.1 65: (ns/day) (hour/ns) 65: Performance: 8.459 2.837 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 20, rlist from 0.749 to 0.843 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 10 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.202 0.101 199.8 65: (ns/day) (hour/ns) 65: Performance: 7.698 3.118 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (457 ms) 65: [----------] 8 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2764 ms total) 65: 65: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.205 0.103 199.9 65: (ns/day) (hour/ns) 65: Performance: 14.311 1.677 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.129 0.064 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.062 1.990 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 19 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.134 0.067 199.8 65: (ns/day) (hour/ns) 65: Performance: 11.583 2.072 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (265 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 13 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.216 0.108 199.9 65: (ns/day) (hour/ns) 65: Performance: 13.597 1.765 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.126 0.063 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.286 1.954 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.102 0.051 199.7 65: (ns/day) (hour/ns) 65: Performance: 15.216 1.577 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (252 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 11 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.240 0.120 199.9 65: (ns/day) (hour/ns) 65: Performance: 12.252 1.959 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.138 0.069 199.8 65: (ns/day) (hour/ns) 65: Performance: 11.252 2.133 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.103 0.051 199.8 65: (ns/day) (hour/ns) 65: Performance: 15.140 1.585 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (265 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.183 0.091 199.9 65: (ns/day) (hour/ns) 65: Performance: 16.075 1.493 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.094 0.047 199.7 65: (ns/day) (hour/ns) 65: Performance: 16.525 1.452 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.071 0.035 199.6 65: (ns/day) (hour/ns) 65: Performance: 21.956 1.093 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (208 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.141 0.071 199.9 65: (ns/day) (hour/ns) 65: Performance: 20.780 1.155 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.075 0.037 199.8 65: (ns/day) (hour/ns) 65: Performance: 20.738 1.157 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 16 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.109 0.055 199.8 65: (ns/day) (hour/ns) 65: Performance: 14.203 1.690 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (181 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.195 0.097 199.9 65: (ns/day) (hour/ns) 65: Performance: 15.073 1.592 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.118 0.059 199.9 65: (ns/day) (hour/ns) 65: Performance: 13.213 1.816 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.108 0.054 199.7 65: (ns/day) (hour/ns) 65: Performance: 14.415 1.665 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (241 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.256 0.128 199.9 65: (ns/day) (hour/ns) 65: Performance: 11.471 2.092 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.142 0.071 199.9 65: (ns/day) (hour/ns) 65: Performance: 10.955 2.191 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.125 0.062 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.444 1.929 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (284 ms) 65: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-05 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.702 nm, buffer size 0.002 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.702 nm, buffer size 0.002 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.232 0.116 199.9 65: (ns/day) (hour/ns) 65: Performance: 12.655 1.896 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.137 0.069 199.9 65: (ns/day) (hour/ns) 65: Performance: 11.338 2.117 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Changing nstlist from 8 to 100, rlist from 0.702 to 0.738 65: 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.138 0.069 199.8 65: (ns/day) (hour/ns) 65: Performance: 11.261 2.131 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (296 ms) 65: [----------] 8 tests from NVT/MdrunNoAppendContinuationIsExact (1996 ms total) 65: 65: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact 65: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.223 0.111 199.9 65: (ns/day) (hour/ns) 65: Performance: 13.191 1.819 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 17 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.127 0.064 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.199 1.967 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 19 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.121 0.061 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.802 1.875 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (263 ms) 65: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 68.810 K for 65: determining the Verlet buffer size 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.241 0.121 199.9 65: (ns/day) (hour/ns) 65: Performance: 12.165 1.973 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.126 0.063 199.9 65: (ns/day) (hour/ns) 65: Performance: 12.306 1.950 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.141 0.071 199.8 65: (ns/day) (hour/ns) 65: Performance: 11.015 2.179 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (286 ms) 65: [----------] 2 tests from NPH/MdrunNoAppendContinuationIsExact (549 ms total) 65: 65: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.217 0.109 199.9 65: (ns/day) (hour/ns) 65: Performance: 13.524 1.775 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 26 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.132 0.066 199.8 65: (ns/day) (hour/ns) 65: Performance: 11.735 2.045 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.122 0.061 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.742 1.883 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (265 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.212 0.106 199.9 65: (ns/day) (hour/ns) 65: Performance: 13.832 1.735 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 17 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.127 0.063 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.256 1.958 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.122 0.061 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.757 1.881 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (252 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.227 0.113 199.9 65: (ns/day) (hour/ns) 65: Performance: 12.956 1.852 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.118 0.059 199.7 65: (ns/day) (hour/ns) 65: Performance: 13.161 1.824 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.107 0.054 199.8 65: (ns/day) (hour/ns) 65: Performance: 14.515 1.653 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (251 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]: 65: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 65: 1 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.219 0.109 199.9 65: (ns/day) (hour/ns) 65: Performance: 13.430 1.787 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 19 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.142 0.071 199.8 65: (ns/day) (hour/ns) 65: Performance: 10.918 2.198 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 28 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.126 0.063 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.369 1.940 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (274 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.220 0.110 199.9 65: (ns/day) (hour/ns) 65: Performance: 13.329 1.801 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.130 0.065 199.9 65: (ns/day) (hour/ns) 65: Performance: 11.954 2.008 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.126 0.063 199.7 65: (ns/day) (hour/ns) 65: Performance: 12.351 1.943 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (268 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 11 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.285 0.143 199.9 65: (ns/day) (hour/ns) 65: Performance: 10.288 2.333 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 16 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.156 0.078 199.9 65: (ns/day) (hour/ns) 65: Performance: 9.982 2.404 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.081 0.040 199.6 65: (ns/day) (hour/ns) 65: Performance: 19.207 1.250 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (293 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 65: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (0 ms) 65: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.234 0.117 199.9 65: (ns/day) (hour/ns) 65: Performance: 12.525 1.916 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.138 0.069 199.9 65: (ns/day) (hour/ns) 65: Performance: 11.269 2.130 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.130 0.065 199.7 65: (ns/day) (hour/ns) 65: Performance: 11.919 2.014 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (273 ms) 65: [----------] 8 tests from NPT/MdrunNoAppendContinuationIsExact (1879 ms total) 65: 65: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact 65: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Number of degrees of freedom in T-Coupling group System is 33.00 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps. 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 1 of the 1 non-bonded parameter combinations 65: 65: Excluding 1 bonded neighbours molecule type 'Argon' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.465 0.232 200.0 65: (ns/day) (hour/ns) 65: Performance: 6.318 3.798 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 12 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.293 0.146 199.9 65: (ns/day) (hour/ns) 65: Performance: 5.312 4.518 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Argon' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.264 0.132 199.9 65: (ns/day) (hour/ns) 65: Performance: 5.890 4.075 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (548 ms) 65: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (548 ms total) 65: 65: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact 65: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.255 0.128 199.9 65: (ns/day) (hour/ns) 65: Performance: 11.500 2.087 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 18 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.155 0.077 199.8 65: (ns/day) (hour/ns) 65: Performance: 10.048 2.388 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 20 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.123 0.062 199.8 65: (ns/day) (hour/ns) 65: Performance: 12.626 1.901 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (312 ms) 65: [ RUN ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There were 3 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'FirstWaterMolecule' has 3 atoms 65: Pull group 2 'SecondWaterMolecule' has 3 atoms 65: Number of degrees of freedom in T-Coupling group System is 9.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 2573.591 K for 65: determining the Verlet buffer size 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 3 2 65: 2 3 5 1.112 nm 1.000 nm 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps. 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 3 of the 3 non-bonded parameter combinations 65: 65: Generated 3 of the 3 1-4 parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.877 nm, buffer size 0.177 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.862 nm, buffer size 0.162 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.313 0.156 199.9 65: (ns/day) (hour/ns) 65: Performance: 9.391 2.556 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 16 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.166 0.083 199.9 65: (ns/day) (hour/ns) 65: Performance: 9.356 2.565 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc2' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.144 0.072 199.8 65: (ns/day) (hour/ns) 65: Performance: 10.772 2.228 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Pull_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Pull/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (347 ms) 65: [----------] 2 tests from Pull/MdrunNoAppendContinuationIsExact (660 ms total) 65: 65: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact 65: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: Setting the AWH bias MC random seed to 2147340147 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'C_&_r_1' has 1 atoms 65: Pull group 2 'N_&_r_2' has 1 atoms 65: Pull group 3 'CA' has 1 atoms 65: Pull group 4 'C_&_r_2' has 1 atoms 65: Pull group 5 'N_&_r_3' has 1 atoms 65: Number of degrees of freedom in T-Coupling group System is 51.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 1 0 65: 2 1 0 179.098 deg 0.000 deg 65: 2 1 0 65: 3 1 0 158.667 deg 0.000 deg 65: 65: There were 3 NOTEs 65: Setting the AWH bias MC random seed to -67407977 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'C_&_r_1' has 1 atoms 65: Pull group 2 'N_&_r_2' has 1 atoms 65: Pull group 3 'CA' has 1 atoms 65: Pull group 4 'C_&_r_2' has 1 atoms 65: Pull group 5 'N_&_r_3' has 1 atoms 65: Number of degrees of freedom in T-Coupling group System is 51.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 1 0 65: 2 1 0 179.098 deg 0.000 deg 65: 2 1 0 65: 3 1 0 158.667 deg 0.000 deg 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.301 0.151 199.9 65: (ns/day) (hour/ns) 65: Performance: 9.748 2.462 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: NOTE: 15 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.170 0.085 199.8 65: (ns/day) (hour/ns) 65: Performance: 9.151 2.623 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: NOTE: 17 % of the run time was spent in pair search, 65: you might want to increase nstlist (this has no effect on accuracy) 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.177 0.088 199.8 65: (ns/day) (hour/ns) 65: Performance: 8.788 2.731 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (420 ms) 65: [ RUN ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 65: Setting the AWH bias MC random seed to 2145336536 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'C_&_r_1' has 1 atoms 65: Pull group 2 'N_&_r_2' has 1 atoms 65: Pull group 3 'CA' has 1 atoms 65: Pull group 4 'C_&_r_2' has 1 atoms 65: Pull group 5 'N_&_r_3' has 1 atoms 65: Number of degrees of freedom in T-Coupling group System is 51.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 1 0 65: 2 1 0 179.098 deg 0.000 deg 65: 2 1 0 65: 3 1 0 158.667 deg 0.000 deg 65: 65: There were 3 NOTEs 65: Setting the AWH bias MC random seed to 2143018103 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: Setting nstcalcenergy (100) equal to nstenergy (4) 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Pull group 1 'C_&_r_1' has 1 atoms 65: Pull group 2 'N_&_r_2' has 1 atoms 65: Pull group 3 'CA' has 1 atoms 65: Pull group 4 'C_&_r_2' has 1 atoms 65: Pull group 5 'N_&_r_3' has 1 atoms 65: Number of degrees of freedom in T-Coupling group System is 51.00 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: Pull group natoms pbc atom distance at start reference at t=0 65: 1 1 0 65: 2 1 0 179.098 deg 0.000 deg 65: 2 1 0 65: 3 1 0 158.667 deg 0.000 deg 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 16 steps, 0.0 ps. 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2145 of the 2145 non-bonded parameter combinations 65: 65: Generated 2145 of the 2145 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.370 0.185 199.9 65: (ns/day) (hour/ns) 65: Performance: 7.932 3.026 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.211 0.106 199.8 65: (ns/day) (hour/ns) 65: Performance: 7.367 3.258 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'Alanine-dipeptide' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.200 0.100 199.8 65: (ns/day) (hour/ns) 65: Performance: 7.788 3.082 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Awh_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] Awh/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (481 ms) 65: [----------] 2 tests from Awh/MdrunNoAppendContinuationIsExact (902 ms total) 65: 65: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact 65: [ RUN ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 65: that with the Verlet scheme, nstlist has no effect on the accuracy of 65: your simulation. 65: 65: Generating 1-4 interactions: fudge = 0.5 65: Number of degrees of freedom in T-Coupling group System is 79.00 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps. 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: Generated 2485 of the 2485 non-bonded parameter combinations 65: 65: Generated 2485 of the 2485 1-4 parameter combinations 65: 65: Excluding 3 bonded neighbours molecule type 'nonanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 65: 65: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.413 0.207 200.0 65: (ns/day) (hour/ns) 65: Performance: 7.106 3.378 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 8 steps, 0.0 ps. 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.240 0.120 199.9 65: (ns/day) (hour/ns) 65: Performance: 6.470 3.710 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun '30 system in water' 65: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps). 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.226 0.113 199.8 65: (ns/day) (hour/ns) 65: Performance: 6.863 3.497 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ExpandedEnsemble_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Last energy frame read 2 time 0.008 Reading energy frame 0 time 0.008 Reading energy frame 1 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 2 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 2 time 0.016 [ OK ] ExpandedEnsemble/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (520 ms) 65: [----------] 1 test from ExpandedEnsemble/MdrunNoAppendContinuationIsExact (520 ms total) 65: 65: [----------] 3 tests from Checking/InitialConstraintsTest 65: [ RUN ] Checking/InitialConstraintsTest.Works/0 65: Number of degrees of freedom in T-Coupling group rest is 11.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 65: NVE simulation: will use the initial temperature of 1141.954 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc-and-methanol' 65: 1 steps, 0.0 ps. 65: Setting the LD random seed to -9961529 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.042 0.021 199.4 65: (ns/day) (hour/ns) 65: Performance: 8.171 2.937 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (48 ms) 65: [ RUN ] Checking/InitialConstraintsTest.Works/1 65: Number of degrees of freedom in T-Coupling group rest is 11.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 65: NVE simulation: will use the initial temperature of 1141.954 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 2 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc-and-methanol' 65: 1 steps, 0.0 ps. 65: Setting the LD random seed to 2130017390 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.065 0.033 199.7 65: (ns/day) (hour/ns) 65: Performance: 5.287 4.539 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (48 ms) 65: [ RUN ] Checking/InitialConstraintsTest.Works/2 65: 65: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 65: Integrator method md-vv-avek is implemented primarily for validation 65: purposes; for molecular dynamics, you should probably be using md or 65: md-vv 65: 65: Number of degrees of freedom in T-Coupling group rest is 11.00 65: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 65: 65: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 65: NVE simulation: will use the initial temperature of 1141.954 K for 65: determining the Verlet buffer size 65: 65: 65: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 65: You are using a plain Coulomb cut-off, which might produce artifacts. 65: You might want to consider using PME electrostatics. 65: 65: 65: 65: There were 3 NOTEs 65: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 65: Can not increase nstlist because an NVE ensemble is used 65: Using 1 MPI process 65: Using 2 OpenMP threads 65: 65: 65: NOTE: The number of threads is not equal to the number of (logical) cpus 65: and the -pin option is set to auto: will not pin threads to cpus. 65: This can lead to significant performance degradation. 65: Consider using -pin on (and -pinoffset in case you run multiple jobs). 65: starting mdrun 'spc-and-methanol' 65: 1 steps, 0.0 ps. 65: Setting the LD random seed to 1474267135 65: 65: Generated 8 of the 10 non-bonded parameter combinations 65: 65: Excluding 2 bonded neighbours molecule type 'Methanol' 65: 65: turning H bonds into constraints... 65: 65: Excluding 2 bonded neighbours molecule type 'SOL' 65: 65: turning H bonds into constraints... 65: 65: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 65: 65: Calculated rlist for 1x1 atom pair-list as 1.126 nm, buffer size 0.126 nm 65: 65: Set rlist, assuming 4x4 atom pair-list, to 1.110 nm, buffer size 0.110 nm 65: 65: Note that mdrun will redetermine rlist based on the actual pair-list setup 65: 65: This run will generate roughly 0 Mb of data 65: 65: Writing final coordinates. 65: 65: Core t (s) Wall t (s) (%) 65: Time: 0.090 0.045 199.7 65: (ns/day) (hour/ns) 65: Performance: 3.832 6.264 65: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 65: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (69 ms) 65: [----------] 3 tests from Checking/InitialConstraintsTest (166 ms total) 65: 65: [----------] Global test environment tear-down 65: [==========] 76 tests from 13 test suites ran. (32672 ms total) 65: [ PASSED ] 76 tests. 65/91 Test #65: MdrunIOTests ................................. Passed 32.82 sec test 66 Start 66: MdrunTestsOneRank 66: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunTestsOneRank.xml" 66: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 66: Test timeout computed to be: 600 66: [==========] Running 28 tests from 7 test suites. 66: [----------] Global test environment set-up. 66: [----------] 1 test from CompelTest 66: [ RUN ] CompelTest.SwapCanRun 66: Setting the LD random seed to 2143279198 66: 66: Generated 330891 of the 330891 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein' 66: 66: turning all bonds into constraints... 66: 66: Excluding 3 bonded neighbours molecule type 'OCT' 66: 66: turning all bonds into constraints... 66: 66: Excluding 1 bonded neighbours molecule type 'NA' 66: 66: turning all bonds into constraints... 66: 66: Excluding 1 bonded neighbours molecule type 'CL' 66: 66: turning all bonds into constraints... 66: 66: Excluding 3 bonded neighbours molecule type 'Protein' 66: 66: Excluding 3 bonded neighbours molecule type 'OCT' 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning all bonds into constraints... 66: Split0 group 'Ch0' contains 83 atoms. 66: Split1 group 'Ch1' contains 83 atoms. 66: Solvent group 'SOL' contains 11931 atoms. 66: Swap group 'NA+' contains 19 atoms. 66: Swap group 'CL-' contains 19 atoms. 66: Number of degrees of freedom in T-Coupling group System is 27869.00 66: 66: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 66: 66: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 66: Removing center of mass motion in the presence of position restraints 66: might cause artifacts. When you are using position restraints to 66: equilibrate a macro-molecule, the artifacts are usually negligible. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 1 Mb of data 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Update groups can not be used for this system because there are three or more consecutively coupled constraints 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: SWAP: Determining initial numbers of ions per compartment. 66: SWAP: Setting pointers for checkpoint writing 66: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 66: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 66: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 66: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 66: starting mdrun 'Channel_coco in octane membrane' 66: 2 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 22 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 1.294 0.647 200.0 66: (ns/day) (hour/ns) 66: Performance: 2.003 11.982 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 66: 66: Update groups can not be used for this system because there are three or more consecutively coupled constraints 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: SWAP: Setting pointers for checkpoint writing 66: SWAP: Copying channel fluxes from checkpoint file data 66: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 66: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 66: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 66: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 66: starting mdrun 'Channel_coco in octane membrane' 66: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 66: 66: Writing final coordinates. 66: 66: NOTE: 21 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.561 0.281 199.9 66: (ns/day) (hour/ns) 66: Performance: 4.619 5.196 66: [ OK ] CompelTest.SwapCanRun (1971 ms) 66: [----------] 1 test from CompelTest (1971 ms total) 66: 66: [----------] 6 tests from BondedInteractionsTest 66: [ RUN ] BondedInteractionsTest.NormalBondWorks 66: Setting the LD random seed to -286067270 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 2 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 40 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.021 0.010 199.4 66: (ns/day) (hour/ns) 66: Performance: 8.251 2.909 66: [ OK ] BondedInteractionsTest.NormalBondWorks (25 ms) 66: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to -701514450 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 2 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 71 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.020 0.010 199.4 66: (ns/day) (hour/ns) 66: Performance: 8.770 2.736 66: [ OK ] BondedInteractionsTest.TabulatedBondWorks (29 ms) 66: [ RUN ] BondedInteractionsTest.NormalAngleWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to 1073445855 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 4 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 23 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.015 0.007 199.2 66: (ns/day) (hour/ns) 66: Performance: 11.819 2.031 66: [ OK ] BondedInteractionsTest.NormalAngleWorks (25 ms) 66: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to 1433390551 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 4 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: 66: This run will generate roughly 0 Mb of data 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 34 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.029 0.015 199.6 66: (ns/day) (hour/ns) 66: Performance: 5.875 4.085 66: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (29 ms) 66: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to -418422935 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 4 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: There were 3 NOTEs 66: 66: This run will generate roughly 0 Mb of data 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 17 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.019 0.010 199.4 66: (ns/day) (hour/ns) 66: Performance: 8.890 2.700 66: [ OK ] BondedInteractionsTest.NormalDihedralWorks (26 ms) 66: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to 2129753980 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'butane' 66: 66: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 66: In moleculetype 'butane' 4 atoms are not bound by a potential or 66: constraint to any other atom in the same moleculetype. Although 66: technically this might not cause issues in a simulation, this often means 66: that the user forgot to add a bond/potential/constraint or put multiple 66: molecules in the same moleculetype definition by mistake. Run with -v to 66: get information for each atom. 66: 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 66: NVE simulation with an initial temperature of zero: will use a Verlet 66: buffer of 10%. Check your energy drift! 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 66: 66: Reading frames from gro file 'A single butane', 4 atoms. 66: Reading frame 0 time 0.000 Last frame 0 time 0.000 66: 66: NOTE: 38 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.009 0.004 198.9 66: (ns/day) (hour/ns) 66: Performance: 19.685 1.219 66: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (20 ms) 66: [----------] 6 tests from BondedInteractionsTest (158 ms total) 66: 66: [----------] 2 tests from BoxDeformationTest 66: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (10) 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 66: For a correct single-point energy evaluation with nsteps = 0, use 66: continuation = yes to avoid constraining the input coordinates. 66: 66: Setting the LD random seed to -100795410 66: 66: Generated 1 of the 1 non-bonded parameter combinations 66: 66: Excluding 1 bonded neighbours molecule type 'Argon' 66: 66: Setting gen_seed to -33641015 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: 66: This run will generate roughly 0 Mb of data 66: Number of degrees of freedom in T-Coupling group rest is 33.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Argon' 66: 0 steps, 0.0 ps. 66: 66: NOTE: 15 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.022 0.011 198.9 66: (ns/day) (hour/ns) 66: Performance: 15.392 1.559 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (10) 66: 66: [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (31 ms) 66: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 66: Setting the LD random seed to 2112569331 66: 66: Generated 330891 of the 330891 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 330891 of the 330891 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: Number of degrees of freedom in T-Coupling group rest is 1293.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 66: 66: Estimate for the relative computational load of the PME mesh part: 0.23 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 2 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 20 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.442 0.221 199.9 66: (ns/day) (hour/ns) 66: Performance: 16.431 1.461 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (3826 ms) 66: [----------] 2 tests from BoxDeformationTest (3871 ms total) 66: 66: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 66: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Setting the LD random seed to -25462921 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 66: 66: Estimate for the relative computational load of the PME mesh part: 0.95 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 2 [file ala.top, line 256]: 66: For energy conservation with LINCS, lincs_iter should be 2 or larger. 66: 66: 66: Number of degrees of freedom in T-Coupling group rest is 54.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'UNNAMED in water' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.047 199.8 66: (ns/day) (hour/ns) 66: Performance: 9.265 2.590 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Setting the LD random seed to -1094714377 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 66: 66: Estimate for the relative computational load of the PME mesh part: 0.95 66: 66: This run will generate roughly 0 Mb of data 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 2 [file ala.top, line 256]: 66: For energy conservation with LINCS, lincs_iter should be 2 or larger. 66: 66: 66: Number of degrees of freedom in T-Coupling group rest is 54.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'UNNAMED in water' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.083 0.042 199.7 66: (ns/day) (hour/ns) 66: Performance: 10.343 2.320 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 trr version: GMX_trn_file (single precision) 66: 66: 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (62710 ms) 66: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Setting the LD random seed to 1528231917 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 66: 66: Estimate for the relative computational load of the PME mesh part: 0.95 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 2 [file ala.top, line 256]: 66: For energy conservation with LINCS, lincs_iter should be 2 or larger. 66: 66: 66: Number of degrees of freedom in T-Coupling group rest is 54.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'UNNAMED in water' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.093 0.047 199.8 66: (ns/day) (hour/ns) 66: Performance: 9.249 2.595 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Setting the LD random seed to 2073753310 66: 66: Generated 2211 of the 2211 non-bonded parameter combinations 66: 66: Generated 2211 of the 2211 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 66: 66: turning H bonds into constraints... 66: 66: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 66: Calculating fourier grid dimensions for X Y Z 66: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 66: 66: Estimate for the relative computational load of the PME mesh part: 0.95 66: 66: This run will generate roughly 0 Mb of data 66: 66: NOTE 2 [file ala.top, line 256]: 66: For energy conservation with LINCS, lincs_iter should be 2 or larger. 66: 66: 66: Number of degrees of freedom in T-Coupling group rest is 54.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 66: The optimal PME mesh load for parallel simulations is below 0.5 66: and for highly parallel simulations between 0.25 and 0.33, 66: for higher performance, increase the cut-off and the PME grid spacing. 66: 66: 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 66: Can not increase nstlist because an NVE ensemble is used 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'UNNAMED in water' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.091 0.046 199.8 66: (ns/day) (hour/ns) 66: Performance: 9.487 2.530 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 66: 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (135 ms) 66: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (62851 ms total) 66: 66: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 66: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: Setting the LD random seed to -688140 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: This run will generate roughly 0 Mb of data 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.040 0.020 199.4 66: (ns/day) (hour/ns) 66: Performance: 21.652 1.108 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Pull group 1 'FirstWaterMolecule' has 3 atoms 66: Pull group 2 'SecondWaterMolecule' has 3 atoms 66: Number of degrees of freedom in T-Coupling group rest is 9.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: Pull group natoms pbc atom distance at start reference at t=0 66: 1 3 2 66: 2 3 5 1.112 nm 1.000 nm 66: Setting the LD random seed to 535822219 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: turning H bonds into constraints... 66: 66: This run will generate roughly 0 Mb of data 66: 66: There was 1 NOTE 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 66: Can not increase nstlist because an NVE ensemble is used 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 4 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.046 0.023 199.5 66: (ns/day) (hour/ns) 66: Performance: 18.773 1.278 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 66: 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 66: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 66: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (61 ms) 66: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (61 ms total) 66: 66: [----------] 12 tests from FreezeWorks/FreezeGroupTest 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.086 0.043 199.7 66: (ns/day) (hour/ns) 66: Performance: 17.976 1.335 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (58 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.089 0.045 199.7 66: (ns/day) (hour/ns) 66: Performance: 17.420 1.378 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (60 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.087 0.043 199.7 66: (ns/day) (hour/ns) 66: Performance: 17.896 1.341 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (59 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.115 0.057 199.8 66: (ns/day) (hour/ns) 66: Performance: 13.526 1.774 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (73 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: NVE simulation: will use the initial temperature of 318.937 K for 66: determining the Verlet buffer size 66: 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 5 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.118 0.059 199.8 66: (ns/day) (hour/ns) 66: Performance: 13.203 1.818 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (75 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 66: ./src/programs/mdrun/tests/freezegroups.cpp:194: Skipped 66: Parrinello-Rahman is not implemented in md-vv. 66: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.107 0.053 199.8 66: (ns/day) (hour/ns) 66: Performance: 14.544 1.650 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (72 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.109 0.055 199.8 66: (ns/day) (hour/ns) 66: Performance: 14.197 1.690 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (74 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.160 0.080 199.8 66: (ns/day) (hour/ns) 66: Performance: 9.737 2.465 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (99 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.085 0.042 199.7 66: (ns/day) (hour/ns) 66: Performance: 18.359 1.307 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (122 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.087 0.044 199.7 66: (ns/day) (hour/ns) 66: Performance: 17.789 1.349 66: 66: 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (85 ms) 66: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 66: Generating 1-4 interactions: fudge = 0.5 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: There are 5 atoms that are fully frozen and part of COMM removal 66: group(s), removing these atoms from the COMM removal group(s) 66: 66: 66: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: There are 3 atoms that are frozen along less then 3 dimensions and part 66: of COMM removal group(s), due to limitations in the code these still 66: contribute to the mass of the COM along frozen dimensions and therefore 66: the COMM correction will be too small. 66: 66: Number of degrees of freedom in T-Coupling group System is 25.50 66: 66: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 66: You are using a plain Coulomb cut-off, which might produce artifacts. 66: You might want to consider using PME electrostatics. 66: 66: 66: 66: There were 4 NOTEs 66: 66: There was 1 WARNING 66: Generated 2145 of the 2145 non-bonded parameter combinations 66: 66: Generated 2145 of the 2145 1-4 parameter combinations 66: 66: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 66: 66: turning H bonds into constraints... 66: 66: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 66: 66: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 66: 66: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 66: 66: Note that mdrun will redetermine rlist based on the actual pair-list setup 66: 66: This run will generate roughly 0 Mb of data 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 66: 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'Alanine-dipeptide' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.085 0.043 199.7 66: (ns/day) (hour/ns) 66: Performance: 18.287 1.312 66: 66: 66: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (75 ms) 66: [----------] 12 tests from FreezeWorks/FreezeGroupTest (860 ms total) 66: 66: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 66: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generating 1-4 interactions: fudge = 0.5 66: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 66: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: Net Acceleration in X direction, will not be corrected 66: Net Acceleration in Y direction, will not be corrected 66: Net Acceleration in Z direction, will not be corrected 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: Generated 3 of the 3 non-bonded parameter combinations 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Setting gen_seed to -1082131473 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: 66: This run will generate roughly 0 Mb of data 66: 66: Writing final coordinates. 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.064 0.032 199.7 66: (ns/day) (hour/ns) 66: Performance: 48.687 0.493 66: 66: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (38 ms) 66: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Setting gen_seed to 921697132 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 66: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 66: Net Acceleration in X direction, will not be corrected 66: Net Acceleration in Y direction, will not be corrected 66: Net Acceleration in Z direction, will not be corrected 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because verlet-buffer-tolerance is not set or used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: NOTE: 11 % of the run time was spent in pair search, 66: you might want to increase nstlist (this has no effect on accuracy) 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.064 0.032 199.6 66: (ns/day) (hour/ns) 66: Performance: 48.159 0.498 66: 66: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (41 ms) 66: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Setting gen_seed to -38675997 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 66: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 66: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 66: Net Acceleration in X direction, will not be corrected 66: Net Acceleration in Y direction, will not be corrected 66: Net Acceleration in Z direction, will not be corrected 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because an NVE ensemble is used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.086 0.043 199.7 66: (ns/day) (hour/ns) 66: Performance: 36.300 0.661 66: 66: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (51 ms) 66: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 66: 66: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 66: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 66: that with the Verlet scheme, nstlist has no effect on the accuracy of 66: your simulation. 66: 66: 66: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 66: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 66: < 0 66: 66: 66: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 66: Setting nstcalcenergy (100) equal to nstenergy (4) 66: 66: Generated 3 of the 3 non-bonded parameter combinations 66: Generating 1-4 interactions: fudge = 0.5 66: 66: Generated 3 of the 3 1-4 parameter combinations 66: 66: Excluding 2 bonded neighbours molecule type 'SOL' 66: 66: Setting gen_seed to -67247633 66: 66: Velocities were taken from a Maxwell distribution at 0 K 66: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 66: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 66: Net Acceleration in X direction, will not be corrected 66: Net Acceleration in Y direction, will not be corrected 66: Net Acceleration in Z direction, will not be corrected 66: 66: This run will generate roughly 0 Mb of data 66: 66: There were 3 NOTEs 66: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 66: Can not increase nstlist because verlet-buffer-tolerance is not set or used 66: Using 1 MPI process 66: Using 2 OpenMP threads 66: 66: 66: NOTE: The number of threads is not equal to the number of (logical) cpus 66: and the -pin option is set to auto: will not pin threads to cpus. 66: This can lead to significant performance degradation. 66: Consider using -pin on (and -pinoffset in case you run multiple jobs). 66: starting mdrun 'spc2' 66: 8 steps, 0.0 ps. 66: 66: Writing final coordinates. 66: 66: Core t (s) Wall t (s) (%) 66: Time: 0.086 0.043 199.7 66: (ns/day) (hour/ns) 66: Performance: 36.283 0.661 66: 66: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (52 ms) 66: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (185 ms total) 66: 66: [----------] Global test environment tear-down 66: [==========] 28 tests from 7 test suites ran. (70010 ms total) 66: [ PASSED ] 27 tests. 66: [ SKIPPED ] 1 test, listed below: 66: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 66/91 Test #66: MdrunTestsOneRank ............................ Passed 70.57 sec test 67 Start 67: MdrunTestsTwoRanks 67: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunTestsTwoRanks.xml" 67: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 67: Test timeout computed to be: 600 67: [==========] Running 28 tests from 7 test suites. 67: [----------] Global test environment set-up. 67: [----------] 1 test from CompelTest 67: [ RUN ] CompelTest.SwapCanRun 67: Setting the LD random seed to -84443457 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'NA' 67: 67: turning all bonds into constraints... 67: 67: Excluding 1 bonded neighbours molecule type 'CL' 67: 67: turning all bonds into constraints... 67: 67: Excluding 3 bonded neighbours molecule type 'Protein' 67: 67: Excluding 3 bonded neighbours molecule type 'OCT' 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning all bonds into constraints... 67: Split0 group 'Ch0' contains 83 atoms. 67: Split1 group 'Ch1' contains 83 atoms. 67: Solvent group 'SOL' contains 11931 atoms. 67: Swap group 'NA+' contains 19 atoms. 67: Swap group 'CL-' contains 19 atoms. 67: Number of degrees of freedom in T-Coupling group System is 27869.00 67: 67: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 67: 67: Calculated rlist for 1x1 atom pair-list as 1.316 nm, buffer size 0.316 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 1.262 nm, buffer size 0.262 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: Removing center of mass motion in the presence of position restraints 67: might cause artifacts. When you are using position restraints to 67: equilibrate a macro-molecule, the artifacts are usually negligible. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: This run will generate roughly 1 Mb of data 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Determining initial numbers of ions per compartment. 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 2 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 23.6%. 67: The balanceable part of the MD step is 17%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 3.9%. 67: 67: 67: NOTE: 41 % of the run time was spent in domain decomposition, 67: 11 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 2.227 0.557 399.9 67: (ns/day) (hour/ns) 67: Performance: 2.328 10.311 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 67: 67: Update groups can not be used for this system because there are three or more consecutively coupled constraints 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: SWAP: Setting pointers for checkpoint writing 67: SWAP: Copying channel fluxes from checkpoint file data 67: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 67: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 67: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 67: starting mdrun 'Channel_coco in octane membrane' 67: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 67: 67: Writing final coordinates. 67: 67: NOTE: 15 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.478 0.120 399.7 67: (ns/day) (hour/ns) 67: Performance: 10.844 2.213 67: [ OK ] CompelTest.SwapCanRun (1452 ms) 67: [----------] 1 test from CompelTest (1459 ms total) 67: 67: [----------] 6 tests from BondedInteractionsTest 67: [ RUN ] BondedInteractionsTest.NormalBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to 2147090383 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 37 % of the run time was spent in domain decomposition, 67: 29 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 5 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.031 0.008 398.6 67: (ns/day) (hour/ns) 67: Performance: 11.161 2.150 67: [ OK ] BondedInteractionsTest.NormalBondWorks (16 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to -134230165 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 2 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 77 % of the run time was spent in domain decomposition, 67: 9 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.102 0.026 399.5 67: (ns/day) (hour/ns) 67: Performance: 3.379 7.103 67: [ OK ] BondedInteractionsTest.TabulatedBondWorks (42 ms) 67: [ RUN ] BondedInteractionsTest.NormalAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to -537428097 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 67 % of the run time was spent in domain decomposition, 67: 16 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.057 0.014 399.2 67: (ns/day) (hour/ns) 67: Performance: 6.099 3.935 67: [ OK ] BondedInteractionsTest.NormalAngleWorks (22 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to 1031752541 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 58 % of the run time was spent in domain decomposition, 67: 20 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.047 0.012 399.0 67: (ns/day) (hour/ns) 67: Performance: 7.341 3.269 67: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (22 ms) 67: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to 1063251956 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 33 % of the run time was spent in domain decomposition, 67: 26 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.035 0.009 398.7 67: (ns/day) (hour/ns) 67: Performance: 9.843 2.438 67: [ OK ] BondedInteractionsTest.NormalDihedralWorks (18 ms) 67: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to -4198407 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'butane' 67: 67: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]: 67: In moleculetype 'butane' 4 atoms are not bound by a potential or 67: constraint to any other atom in the same moleculetype. Although 67: technically this might not cause issues in a simulation, this often means 67: that the user forgot to add a bond/potential/constraint or put multiple 67: molecules in the same moleculetype definition by mistake. Run with -v to 67: get information for each atom. 67: 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 67: NVE simulation with an initial temperature of zero: will use a Verlet 67: buffer of 10%. Check your energy drift! 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/butane1.gro' 67: 67: Reading frames from gro file 'A single butane', 4 atoms. 67: Reading frame 0 time 0.000 Last frame 0 time 0.000 67: 67: NOTE: 30 % of the run time was spent in domain decomposition, 67: 29 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.038 0.009 398.9 67: (ns/day) (hour/ns) 67: Performance: 9.141 2.626 67: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (34 ms) 67: [----------] 6 tests from BondedInteractionsTest (167 ms total) 67: 67: [----------] 2 tests from BoxDeformationTest 67: [ RUN ] BoxDeformationTest.flowDoesNotAffectEkin 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin_input.mdp]: 67: For a correct single-point energy evaluation with nsteps = 0, use 67: continuation = yes to avoid constraining the input coordinates. 67: 67: Setting the LD random seed to -537497805 67: 67: Generated 1 of the 1 non-bonded parameter combinations 67: 67: Excluding 1 bonded neighbours molecule type 'Argon' 67: 67: Setting gen_seed to -22022785 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: Number of degrees of freedom in T-Coupling group rest is 33.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Argon' 67: 0 steps, 0.0 ps. 67: 67: NOTE: 29 % of the run time was spent in domain decomposition, 67: 24 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.038 0.009 397.0 67: (ns/day) (hour/ns) 67: Performance: 18.263 1.314 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_flowDoesNotAffectEkin.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] BoxDeformationTest.flowDoesNotAffectEkin (20 ms) 67: [ RUN ] BoxDeformationTest.EnergiesWithinTolerances 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (10) 67: 67: Setting the LD random seed to 1597739709 67: 67: Generated 330891 of the 330891 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 330891 of the 330891 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: Number of degrees of freedom in T-Coupling group rest is 1293.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: The largest distance between excluded atoms is 0.152 nm between atom 41 and 42 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 16x16x16, spacing 0.116 0.116 0.116 67: 67: Estimate for the relative computational load of the PME mesh part: 0.23 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 2 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 20 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB got disabled because it was unsuitable to use. 67: Average load imbalance: 12.5%. 67: The balanceable part of the MD step is 30%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 3.7%. 67: 67: 67: Core t (s) Wall t (s) (%) 67: Time: 1.248 0.312 399.9 67: (ns/day) (hour/ns) 67: Performance: 11.631 2.063 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BoxDeformationTest_EnergiesWithinTolerances.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.020 Reading energy frame 2 time 0.040 Last energy frame read 2 time 0.040 [ OK ] BoxDeformationTest.EnergiesWithinTolerances (2388 ms) 67: [----------] 2 tests from BoxDeformationTest (2411 ms total) 67: 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to 2138272703 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.95 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 11 % of the run time was spent in domain decomposition, 67: 2 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.432 0.108 399.7 67: (ns/day) (hour/ns) 67: Performance: 4.000 6.000 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Setting the LD random seed to -1075578946 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: There were 3 NOTEs 67: 67: Estimate for the relative computational load of the PME mesh part: 0.95 67: 67: This run will generate roughly 0 Mb of data 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 6 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.252 0.063 399.5 67: (ns/day) (hour/ns) 67: Performance: 6.859 3.499 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 trr version: GMX_trn_file (single precision) 67: Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: trr version: GMX_trn_file (single precision) 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/0 (53900 ms) 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 67: Setting the LD random seed to -67127813 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.95 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 13 % of the run time was spent in domain decomposition, 67: 3 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.357 0.089 399.7 67: (ns/day) (hour/ns) 67: Performance: 4.833 4.966 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to -201596931 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 2 [file ala.top, line 256]: 67: For energy conservation with LINCS, lincs_iter should be 2 or larger. 67: 67: 67: Number of degrees of freedom in T-Coupling group rest is 54.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_input.mdp]: 67: The optimal PME mesh load for parallel simulations is below 0.5 67: and for highly parallel simulations between 0.25 and 0.33, 67: for higher performance, increase the cut-off and the PME grid spacing. 67: 67: 67: 67: There were 3 NOTEs 67: 67: Generated 2211 of the 2211 non-bonded parameter combinations 67: 67: Generated 2211 of the 2211 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 67: 67: turning H bonds into constraints... 67: 67: The largest distance between excluded atoms is 0.384 nm between atom 5 and 15 67: Calculating fourier grid dimensions for X Y Z 67: Using a fourier grid of 24x24x24, spacing 0.104 0.104 0.104 67: 67: Estimate for the relative computational load of the PME mesh part: 0.95 67: 67: This run will generate roughly 0 Mb of data 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'UNNAMED in water' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: NOTE: 20 % of the run time was spent in domain decomposition, 67: 4 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.260 0.065 399.5 67: (ns/day) (hour/ns) 67: Performance: 6.627 3.622 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeStepping_MtsComparisonTest_WithinTolerances_1_sim2.edr as single precision energy file 67: [ OK ] MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest.WithinTolerances/1 (212 ms) 67: [----------] 2 tests from MultipleTimeSteppingIsNearSingleTimeStepping/MtsComparisonTest (54113 ms total) 67: 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest 67: [ RUN ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to -100688429 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: 67: This run will generate roughly 0 Mb of data 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.125 0.031 399.0 67: (ns/day) (hour/ns) 67: Performance: 13.831 1.735 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: Setting the LD random seed to 2146138629 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: turning H bonds into constraints... 67: Pull group 1 'FirstWaterMolecule' has 3 atoms 67: Pull group 2 'SecondWaterMolecule' has 3 atoms 67: Number of degrees of freedom in T-Coupling group rest is 9.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Pull group natoms pbc atom distance at start reference at t=0 67: 1 3 2 67: 2 3 5 1.112 nm 1.000 nm 67: 67: There was 1 NOTE 67: 67: This run will generate roughly 0 Mb of data 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Multiple time stepping is only supported with GPUs when MTS is only applied to longrange-nonbonded forces. 67: Can not increase nstlist because an NVE ensemble is used 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 4 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.149 0.037 399.2 67: (ns/day) (hour/ns) 67: Performance: 11.582 2.072 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim1.edr as single precision energy file 67: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MultipleTimeSteppingIsNearSingleTimeSteppingPull_MtsComparisonTest_WithinTolerances_0_sim2.edr as single precision energy file 67: [ OK ] MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest.WithinTolerances/0 (100 ms) 67: [----------] 1 test from MultipleTimeSteppingIsNearSingleTimeSteppingPull/MtsComparisonTest (100 ms total) 67: 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 67: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Last energy frame read 1 time 0.004 Last energy frame read 1 time 0.004 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: 67: This run will generate roughly 0 Mb of data 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 1.9%. 67: The balanceable part of the MD step is 67%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 1.3%. 67: 67: 67: NOTE: 15 % of the run time was spent in domain decomposition, 67: 6 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.241 0.061 398.6 67: (ns/day) (hour/ns) 67: Performance: 12.849 1.868 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/0 (82 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: 67: This run will generate roughly 0 Mb of data 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 1.4%. 67: The balanceable part of the MD step is 68%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 1.0%. 67: 67: 67: NOTE: 14 % of the run time was spent in domain decomposition, 67: 6 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.244 0.061 399.3 67: (ns/day) (hour/ns) 67: Performance: 12.747 1.883 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/1 (78 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 1.3%. 67: The balanceable part of the MD step is 68%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.9%. 67: 67: 67: NOTE: 15 % of the run time was spent in domain decomposition, 67: 6 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.239 0.060 399.5 67: (ns/day) (hour/ns) 67: Performance: 13.023 1.843 67: 67: 67: 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/2 (78 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 0.7%. 67: The balanceable part of the MD step is 70%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.5%. 67: 67: 67: NOTE: 12 % of the run time was spent in domain decomposition, 67: 5 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.296 0.074 399.6 67: (ns/day) (hour/ns) 67: Performance: 10.492 2.287 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/3 (92 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 318.937 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: NVE simulation: will use the initial temperature of 318.937 K for 67: determining the Verlet buffer size 67: 67: 67: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 5 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 0.6%. 67: The balanceable part of the MD step is 70%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.4%. 67: 67: 67: NOTE: 12 % of the run time was spent in domain decomposition, 67: 5 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: NOTE: 6 % of the run time was spent communicating energies, 67: you might want to increase some nst* mdp options 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.302 0.075 399.6 67: (ns/day) (hour/ns) 67: Performance: 10.301 2.330 67: 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/4 (93 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 (0 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.263 0.066 399.6 67: (ns/day) (hour/ns) 67: Performance: 11.822 2.030 67: 67: 67: 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/6 (86 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.266 0.067 397.3 67: (ns/day) (hour/ns) 67: Performance: 11.605 2.068 67: 67: 67: 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/7 (87 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.761 nm, buffer size 0.061 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: Generating 1-4 interactions: fudge = 0.5 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 20, rlist from 0.754 to 0.856 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.587 0.147 399.2 67: (ns/day) (hour/ns) 67: Performance: 5.293 4.534 67: 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/8 (183 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.252 0.063 399.4 67: (ns/day) (hour/ns) 67: Performance: 12.302 1.951 67: 67: 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generating 1-4 interactions: fudge = 0.5 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/9 (100 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: This run will generate roughly 0 Mb of data 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.263 0.066 398.2 67: (ns/day) (hour/ns) 67: Performance: 11.767 2.040 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/10 (107 ms) 67: [ RUN ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 2145 of the 2145 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 2145 of the 2145 1-4 parameter combinations 67: 67: Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' 67: 67: turning H bonds into constraints... 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 5 atoms that are fully frozen and part of COMM removal 67: group(s), removing these atoms from the COMM removal group(s) 67: 67: 67: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: There are 3 atoms that are frozen along less then 3 dimensions and part 67: of COMM removal group(s), due to limitations in the code these still 67: contribute to the mass of the COM along frozen dimensions and therefore 67: the COMM correction will be too small. 67: 67: Number of degrees of freedom in T-Coupling group System is 25.50 67: 67: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 67: 67: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 67: 67: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 67: 67: Note that mdrun will redetermine rlist based on the actual pair-list setup 67: 67: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11_input.mdp]: 67: You are using a plain Coulomb cut-off, which might produce artifacts. 67: You might want to consider using PME electrostatics. 67: 67: 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 4 NOTEs 67: 67: There was 1 WARNING 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/FreezeWorks_FreezeGroupTest_WithinTolerances_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Changing nstlist from 8 to 100, rlist from 0.734 to 0.829 67: 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'Alanine-dipeptide' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.253 0.064 398.2 67: (ns/day) (hour/ns) 67: Performance: 12.240 1.961 67: 67: 67: 67: 67: [ OK ] FreezeWorks/FreezeGroupTest.WithinTolerances/11 (112 ms) 67: [----------] 12 tests from FreezeWorks/FreezeGroupTest (1104 ms total) 67: 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -822256445 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 0.6%. 67: The balanceable part of the MD step is 62%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.4%. 67: 67: 67: NOTE: 13 % of the run time was spent in domain decomposition, 67: 8 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.197 0.049 399.3 67: (ns/day) (hour/ns) 67: Performance: 31.447 0.763 67: 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/0 (62 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to -42238213 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 0.0%. 67: The balanceable part of the MD step is 69%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.0%. 67: 67: 67: NOTE: 14 % of the run time was spent in domain decomposition, 67: 9 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.181 0.045 399.3 67: (ns/day) (hour/ns) 67: Performance: 34.341 0.699 67: 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/1 (57 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 631209790 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because an NVE ensemble is used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 0.0%. 67: The balanceable part of the MD step is 71%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 0.0%. 67: 67: 67: NOTE: 12 % of the run time was spent in domain decomposition, 67: 7 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.223 0.056 399.4 67: (ns/day) (hour/ns) 67: Performance: 27.860 0.861 67: 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/2 (67 ms) 67: [ RUN ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 67: 67: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 67: that with the Verlet scheme, nstlist has no effect on the accuracy of 67: your simulation. 67: 67: 67: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: verlet-buffer-pressure-tolerance is ignored when verlet-buffer-tolerance 67: < 0 67: 67: 67: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3_input.mdp]: 67: Setting nstcalcenergy (100) equal to nstenergy (4) 67: 67: Generated 3 of the 3 non-bonded parameter combinations 67: Generating 1-4 interactions: fudge = 0.5 67: 67: Generated 3 of the 3 1-4 parameter combinations 67: 67: Excluding 2 bonded neighbours molecule type 'SOL' 67: 67: Setting gen_seed to 1609677749 67: 67: Velocities were taken from a Maxwell distribution at 0 K 67: Number of degrees of freedom in T-Coupling group FirstWaterMolecule is 6.00 67: Number of degrees of freedom in T-Coupling group SecondWaterMolecule is 6.00 67: Net Acceleration in X direction, will not be corrected 67: Net Acceleration in Y direction, will not be corrected 67: Net Acceleration in Z direction, will not be corrected 67: 67: This run will generate roughly 0 Mb of data 67: 67: There were 3 NOTEs 67: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/AccelerationWorks_AccelerationGroupTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 67: Can not increase nstlist because verlet-buffer-tolerance is not set or used 67: Using 2 MPI processes 67: Using 2 OpenMP threads per MPI process 67: 67: 67: NOTE: The number of threads is not equal to the number of (logical) cpus 67: and the -pin option is set to auto: will not pin threads to cpus. 67: This can lead to significant performance degradation. 67: Consider using -pin on (and -pinoffset in case you run multiple jobs). 67: starting mdrun 'spc2' 67: 8 steps, 0.0 ps. 67: 67: Writing final coordinates. 67: 67: 67: Dynamic load balancing report: 67: DLB was off during the run due to low measured imbalance. 67: Average load imbalance: 6.4%. 67: The balanceable part of the MD step is 61%, load imbalance is computed from this. 67: Part of the total run time spent waiting due to load imbalance: 3.9%. 67: 67: 67: NOTE: 12 % of the run time was spent in domain decomposition, 67: 6 % of the run time was spent in pair search, 67: you might want to increase nstlist (this has no effect on accuracy) 67: 67: Core t (s) Wall t (s) (%) 67: Time: 0.291 0.073 399.6 67: (ns/day) (hour/ns) 67: Performance: 21.343 1.125 67: 67: 67: [ OK ] AccelerationWorks/AccelerationGroupTest.WithinTolerances/3 (85 ms) 67: [----------] 4 tests from AccelerationWorks/AccelerationGroupTest (274 ms total) 67: 67: [----------] Global test environment tear-down 67: [==========] 28 tests from 7 test suites ran. (59679 ms total) 67: [ PASSED ] 27 tests. 67: [ SKIPPED ] 1 test, listed below: 67: [ SKIPPED ] FreezeWorks/FreezeGroupTest.WithinTolerances/5 67/91 Test #67: MdrunTestsTwoRanks ........................... Passed 60.19 sec test 68 Start 68: MdrunSingleRankAlgorithmsTests 68: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-single-rank-algorithms-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunSingleRankAlgorithmsTests.xml" 68: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 68: Test timeout computed to be: 600 68: [==========] Running 5 tests from 3 test suites. 68: [----------] Global test environment set-up. 68: [----------] 1 test from DispersionCorrectionTest 68: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 30.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 68: There are 9 non-linear virtual site constructions. Their contribution to 68: the energy error is approximated. In most cases this does not affect the 68: error significantly. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Changing nstlist from 10 to 40, rlist from 1.023 to 1.158 68: 68: Update groups can not be used for this system because an incompatible virtual site type is used 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Alanine dipeptide in vacuo' 68: 200 steps, 0.4 ps. 68: Setting the LD random seed to -67379485 68: 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 68: 68: turning H bonds into constraints... 68: 68: Cleaning up constraints and constant bonded interactions with virtual sites 68: 68: Converted 3 Bonds with virtual sites to connections, 7 left 68: 68: Removed 18 Angles with virtual sites, 21 left 68: 68: Removed 10 Proper Dih.s with virtual sites, 44 left 68: 68: Converted 12 Constraints with virtual sites to connections, 0 left 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.023 nm, buffer size 0.023 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.392 0.196 199.9 68: (ns/day) (hour/ns) 68: Performance: 177.039 0.136 68: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (431 ms) 68: [----------] 1 test from DispersionCorrectionTest (431 ms total) 68: 68: [----------] 1 test from OriresTest 68: [ RUN ] OriresTest.OriresCanRun 68: Generating 1-4 interactions: fudge = 0.5 68: Number of degrees of freedom in T-Coupling group System is 518.00 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]: 68: You are using a plain Coulomb cut-off, which might produce artifacts. 68: You might want to consider using PME electrostatics. 68: 68: 68: 68: There was 1 NOTE 68: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Changing nstlist from 10 to 25, rlist from 1.07 to 1.203 68: 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1' 68: 10 steps, 0.0 ps. 68: Setting the LD random seed to -171479062 68: 68: Generated 2145 of the 2145 non-bonded parameter combinations 68: 68: Generated 2145 of the 2145 1-4 parameter combinations 68: 68: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 68: 68: turning H bonds into constraints... 68: 68: Excluding 2 bonded neighbours molecule type 'SOL' 68: 68: turning H bonds into constraints... 68: 68: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 68: 68: Calculated rlist for 1x1 atom pair-list as 1.093 nm, buffer size 0.093 nm 68: 68: Set rlist, assuming 4x4 atom pair-list, to 1.070 nm, buffer size 0.070 nm 68: 68: Note that mdrun will redetermine rlist based on the actual pair-list setup 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.158 0.079 199.8 68: (ns/day) (hour/ns) 68: Performance: 24.076 0.997 68: [ OK ] OriresTest.OriresCanRun (534 ms) 68: [----------] 1 test from OriresTest (534 ms total) 68: 68: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest 68: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 68: Number of degrees of freedom in T-Coupling group rest is 10.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 2 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Dipoles' 68: 20 steps, 0.1 ps. 68: Setting the LD random seed to -134299657 68: 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Dipole' 68: 68: Searching the wall atom type(s) 68: 68: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 20x20x40, spacing 0.200 0.200 0.200 68: 68: Estimate for the relative computational load of the PME mesh part: 1.00 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 1.034 0.517 200.0 68: (ns/day) (hour/ns) 68: Performance: 8.773 2.736 68: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_0.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 trr version: GMX_trn_file (single precision) 68: 68: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/0 (77536 ms) 68: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 68: Test system 'epsilon-surface-constraint' cannot run with 1 ranks. 68: The supported numbers are > 1. 68: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/1 (0 ms) 68: [ RUN ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 68: 68: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 68: With epsilon_surface > 0 all molecules should be neutral. 68: 68: 68: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 68: With epsilon_surface > 0 you can only use domain decomposition when there 68: are only small molecules with all bonds constrained (mdrun will check for 68: this). 68: 68: Number of degrees of freedom in T-Coupling group rest is 9.00 68: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 68: 68: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 68: NVE simulation with an initial temperature of zero: will use a Verlet 68: buffer of 10%. Check your energy drift! 68: 68: 68: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2_input.mdp]: 68: The optimal PME mesh load for parallel simulations is below 0.5 68: and for highly parallel simulations between 0.25 and 0.33, 68: for higher performance, increase the cut-off and the PME grid spacing. 68: 68: 68: 68: There were 4 NOTEs 68: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 68: Can not increase nstlist because an NVE ensemble is used 68: Using 1 MPI process 68: Using 2 OpenMP threads 68: 68: 68: NOTE: The number of threads is not equal to the number of (logical) cpus 68: and the -pin option is set to auto: will not pin threads to cpus. 68: This can lead to significant performance degradation. 68: Consider using -pin on (and -pinoffset in case you run multiple jobs). 68: starting mdrun 'Dipoles' 68: 20 steps, 0.1 ps. 68: Setting the LD random seed to 1469964231 68: 68: Generated 1 of the 1 non-bonded parameter combinations 68: 68: Excluding 1 bonded neighbours molecule type 'Dipole' 68: 68: The largest distance between excluded atoms is 0.344 nm between atom 1 and 2 68: Calculating fourier grid dimensions for X Y Z 68: Using a fourier grid of 20x20x20, spacing 0.200 0.200 0.200 68: 68: Estimate for the relative computational load of the PME mesh part: 1.00 68: 68: This run will generate roughly 0 Mb of data 68: 68: Writing final coordinates. 68: 68: Core t (s) Wall t (s) (%) 68: Time: 0.481 0.240 199.9 68: (ns/day) (hour/ns) 68: Performance: 18.875 1.272 68: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EwaldSurfaceTerm_EwaldSurfaceTermTest_WithinTolerances_2.edr as single precision energy file 68: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.010 Reading energy frame 2 time 0.020 Reading energy frame 3 time 0.030 Reading energy frame 4 time 0.040 Reading energy frame 5 time 0.050 Last energy frame read 5 time 0.050 68: [ OK ] EwaldSurfaceTerm/EwaldSurfaceTermTest.WithinTolerances/2 (36624 ms) 68: [----------] 3 tests from EwaldSurfaceTerm/EwaldSurfaceTermTest (114161 ms total) 68: 68: [----------] Global test environment tear-down 68: [==========] 5 tests from 3 test suites ran. (115140 ms total) 68: [ PASSED ] 5 tests. 68/91 Test #68: MdrunSingleRankAlgorithmsTests ............... Passed 115.43 sec test 69 Start 69: Minimize1RankTests 69: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Minimize1RankTests.xml" 69: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 69: Test timeout computed to be: 600 69: [==========] Running 12 tests from 2 test suites. 69: [----------] Global test environment set-up. 69: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -4.7990997e+01 69: Maximum force = 1.8629692e+02 on atom 13 69: Norm of force = 8.7721836e+01 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (239 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 330891 of the 330891 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 0.5 69: 69: Generated 330891 of the 330891 1-4 parameter combinations 69: 69: Excluding 2 bonded neighbours molecule type 'SOL' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 3.02331e+02 on atom 3 69: F-Norm = 1.18024e+02 69: 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -5.5862350e+01 69: Maximum force = 4.2726685e+02 on atom 13 69: Norm of force = 1.8452681e+02 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (732 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: 69: turning H bonds into constraints... 69: Number of degrees of freedom in T-Coupling group System is 22.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = 3.1937723e+02 69: Maximum force = 9.9988691e+03 on atom 9 69: Norm of force = 4.6167015e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (124 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: 69: turning H bonds into constraints... 69: 69: NOTE 3 [file glycine_vacuo.top, line 12]: 69: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 69: 69: Number of degrees of freedom in T-Coupling group System is 22.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 5 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 2.41575e+04 on atom 10 69: F-Norm = 1.18451e+04 69: 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = 1.5174414e+02 69: Maximum force = 7.4208760e+03 on atom 9 69: Norm of force = 3.5692977e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (133 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 69: Generating 1-4 interactions: fudge = 0.5 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 5 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: This run will generate roughly 0 Mb of data 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -1.5698444e+02 69: Maximum force = 4.5702216e+02 on atom 17 69: Norm of force = 1.8327095e+02 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (106 ms) 69: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generating 1-4 interactions: fudge = 0.5 69: Generated 2145 of the 2145 non-bonded parameter combinations 69: 69: Generated 2145 of the 2145 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 69: 69: turning all bonds into constraints... 69: 69: Cleaning up constraints and constant bonded interactions with virtual sites 69: 69: Removed 18 Angles with virtual sites, 21 left 69: 69: Removed 10 Proper Dih.s with virtual sites, 44 left 69: 69: Converted 15 Constraints with virtual sites to connections, 7 left 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 3 [file unknown]: 69: You are using constraints on all bonds, whereas the forcefield has been 69: parametrized only with constraints involving hydrogen atoms. We suggest 69: using constraints = h-bonds instead, this will also improve performance. 69: 69: 69: NOTE 4 [file unknown]: 69: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 69: 69: Number of degrees of freedom in T-Coupling group System is 23.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 6 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Update groups can not be used for this system because an incompatible virtual site type is used 69: 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 1.06799e+03 on atom 28 69: F-Norm = 4.26914e+02 69: 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = -1.6941235e+02 69: Maximum force = 2.1838167e+02 on atom 17 69: Norm of force = 7.9235206e+01 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (114 ms) 69: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1452 ms total) 69: 69: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 3 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents converged to Fmax < 10 in 1 steps 69: Potential Energy = -9.7425687e-01 69: Maximum force = 4.0132279e+00 on atom 1 69: Norm of force = 1.6383933e+00 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 3 NOTEs 69: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (9 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 4.01323e+00 on atom 1 69: F-Norm = 1.63839e+00 69: 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 69: Potential Energy = -9.9064195e-01 69: Maximum force = 2.5781672e+00 on atom 1 69: Norm of force = 1.0525324e+00 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 69: 69: Number of degrees of freedom in T-Coupling group System is 33.00 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 3 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (11 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 69: Generated 1 of the 1 non-bonded parameter combinations 69: 69: Excluding 1 bonded neighbours molecule type 'Argon' 69: 69: This run will generate roughly 0 Mb of data 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Low-Memory BFGS Minimizer: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: Using 10 BFGS correction steps. 69: 69: F-max = 4.01323e+00 on atom 1 69: F-Norm = 1.63839e+00 69: 69: 69: writing lowest energy coordinates. 69: 69: Low-Memory BFGS Minimizer converged to Fmax < 10 in -1 steps 69: Potential Energy = -9.9064195e-01 69: Maximum force = 2.5781672e+00 on atom 1 69: Norm of force = 1.0525324e+00 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (11 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Steepest Descents: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Steepest Descents did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = 3.1939673e+02 69: Maximum force = 9.9704229e+03 on atom 9 69: Norm of force = 4.6227534e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (76 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: 69: This run will generate roughly 0 Mb of data 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Polak-Ribiere Conjugate Gradients: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: F-max = 2.41672e+04 on atom 10 69: F-Norm = 1.19357e+04 69: 69: 69: Energy minimization reached the maximum number of steps before the forces 69: reached the requested precision Fmax < 10. 69: 69: writing lowest energy coordinates. 69: 69: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 69: Potential Energy = 1.5625757e+02 69: Maximum force = 7.5018237e+03 on atom 9 69: Norm of force = 3.6139019e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (80 ms) 69: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 69: 69: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 69: that with the Verlet scheme, nstlist has no effect on the accuracy of 69: your simulation. 69: 69: 69: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 69: setting nstcomm equal to nstcalcenergy for less overhead 69: 69: 69: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 69: 69: Generated 20503 of the 20503 non-bonded parameter combinations 69: Generating 1-4 interactions: fudge = 1 69: 69: Generated 17396 of the 20503 1-4 parameter combinations 69: 69: Excluding 3 bonded neighbours molecule type 'Glycine' 69: Number of degrees of freedom in T-Coupling group System is 27.00 69: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 69: 69: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: You are using a plain Coulomb cut-off, which might produce artifacts. 69: You might want to consider using PME electrostatics. 69: 69: 69: 69: This run will generate roughly 0 Mb of data 69: 69: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 69: COM removal frequency is set to (4). 69: Other settings require a global communication frequency of 100. 69: Note that this will require additional global communication steps, 69: which will reduce performance when using multiple ranks. 69: Consider setting nstcomm to a multiple of 100. 69: 69: 69: There were 4 NOTEs 69: 69: There was 1 WARNING 69: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 69: Using 1 MPI process 69: Using 2 OpenMP threads 69: 69: 69: NOTE: The number of threads is not equal to the number of (logical) cpus 69: and the -pin option is set to auto: will not pin threads to cpus. 69: This can lead to significant performance degradation. 69: Consider using -pin on (and -pinoffset in case you run multiple jobs). 69: 69: Low-Memory BFGS Minimizer: 69: Tolerance (Fmax) = 1.00000e+01 69: Number of steps = 4 69: Using 10 BFGS correction steps. 69: 69: F-max = 2.41672e+04 on atom 10 69: F-Norm = 1.19357e+04 69: 69: 69: Energy minimization has stopped, but the forces have not converged to the 69: requested precision Fmax < 10 (which may not be possible for your system). It 69: stopped because the algorithm tried to make a new step whose size was too 69: small, or there was no change in the energy since last step. Either way, we 69: regard the minimization as converged to within the available machine 69: precision, given your starting configuration and EM parameters. 69: 69: Double precision normally gives you higher accuracy, but this is often not 69: needed for preparing to run molecular dynamics. 69: 69: writing lowest energy coordinates. 69: 69: Low-Memory BFGS Minimizer converged to machine precision in 0 steps, 69: but did not reach the requested Fmax < 10. 69: Potential Energy = 5.6111578e+02 69: Maximum force = 1.2685402e+04 on atom 10 69: Norm of force = 6.0643536e+03 69: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 69: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (79 ms) 69: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (276 ms total) 69: 69: [----------] Global test environment tear-down 69: [==========] 12 tests from 2 test suites ran. (1738 ms total) 69: [ PASSED ] 12 tests. 69/91 Test #69: Minimize1RankTests ........................... Passed 1.99 sec test 70 Start 70: Minimize2RankTests 70: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/minimize-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/Minimize2RankTests.xml" 70: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 70: Test timeout computed to be: 600 70: [==========] Running 12 tests from 2 test suites. 70: [----------] Global test environment set-up. 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -4.7990952e+01 70: Maximum force = 1.8629709e+02 on atom 13 70: Norm of force = 8.7721970e+01 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (453 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 330891 of the 330891 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 330891 of the 330891 1-4 parameter combinations 70: 70: Excluding 2 bonded neighbours molecule type 'SOL' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 3.02331e+02 on atom 3 70: F-Norm = 1.18024e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -5.5862202e+01 70: Maximum force = 4.2727243e+02 on atom 13 70: Norm of force = 1.8452909e+02 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (279 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: turning H bonds into constraints... 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.1937720e+02 70: Maximum force = 9.9988691e+03 on atom 9 70: Norm of force = 4.6167015e+03 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (198 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: 70: Generating 1-4 interactions: fudge = 1 70: turning H bonds into constraints... 70: 70: NOTE 3 [file glycine_vacuo.top, line 12]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: Number of degrees of freedom in T-Coupling group System is 22.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41575e+04 on atom 10 70: F-Norm = 1.18451e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.5174358e+02 70: Maximum force = 7.4208833e+03 on atom 9 70: Norm of force = 3.5692986e+03 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (365 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: 70: Generating 1-4 interactions: fudge = 0.5 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 5 NOTEs 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.5698444e+02 70: Maximum force = 4.5702219e+02 on atom 17 70: Norm of force = 1.8327095e+02 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 3.000 Last energy frame read 2 time 3.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (260 ms) 70: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 70: Generated 2145 of the 2145 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 0.5 70: 70: Generated 2145 of the 2145 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 70: 70: turning all bonds into constraints... 70: 70: NOTE 3 [file unknown]: 70: You are using constraints on all bonds, whereas the forcefield has been 70: parametrized only with constraints involving hydrogen atoms. We suggest 70: using constraints = h-bonds instead, this will also improve performance. 70: 70: 70: NOTE 4 [file unknown]: 70: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 70: 70: 70: Cleaning up constraints and constant bonded interactions with virtual sites 70: 70: Removed 18 Angles with virtual sites, 21 left 70: 70: Removed 10 Proper Dih.s with virtual sites, 44 left 70: 70: Converted 15 Constraints with virtual sites to connections, 7 left 70: Number of degrees of freedom in T-Coupling group System is 23.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 6 NOTEs 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Update groups can not be used for this system because an incompatible virtual site type is used 70: 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 1.06799e+03 on atom 28 70: F-Norm = 4.26914e+02 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = -1.6941229e+02 70: Maximum force = 2.1838167e+02 on atom 17 70: Norm of force = 7.9235200e+01 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (340 ms) 70: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1909 ms total) 70: 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents converged to Fmax < 10 in 1 steps 70: Potential Energy = -9.7425687e-01 70: Maximum force = 4.0132279e+00 on atom 3 70: Norm of force = 1.6383933e+00 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (392 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 4.01323e+00 on atom 3 70: F-Norm = 1.63839e+00 70: 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 70: Potential Energy = -9.9064195e-01 70: Maximum force = 2.5781672e+00 on atom 3 70: Norm of force = 1.0525324e+00 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Number of degrees of freedom in T-Coupling group System is 33.00 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 3 NOTEs 70: 70: There was 1 WARNING 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (248 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 70: Generated 1 of the 1 non-bonded parameter combinations 70: 70: Excluding 1 bonded neighbours molecule type 'Argon' 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (2 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: This run will generate roughly 0 Mb of data 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Steepest Descents: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Steepest Descents did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 3.1939664e+02 70: Maximum force = 9.9704229e+03 on atom 9 70: Norm of force = 4.6227537e+03 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 1.000 Reading energy frame 2 time 2.000 Reading energy frame 3 time 3.000 Reading energy frame 4 time 4.000 Last energy frame read 4 time 4.000 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (194 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: 70: This run will generate roughly 0 Mb of data 70: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 70: Using 2 MPI processes 70: Using 2 OpenMP threads per MPI process 70: 70: 70: NOTE: The number of threads is not equal to the number of (logical) cpus 70: and the -pin option is set to auto: will not pin threads to cpus. 70: This can lead to significant performance degradation. 70: Consider using -pin on (and -pinoffset in case you run multiple jobs). 70: 70: Polak-Ribiere Conjugate Gradients: 70: Tolerance (Fmax) = 1.00000e+01 70: Number of steps = 4 70: F-max = 2.41672e+04 on atom 10 70: F-Norm = 1.19357e+04 70: 70: 70: Energy minimization reached the maximum number of steps before the forces 70: reached the requested precision Fmax < 10. 70: 70: writing lowest energy coordinates. 70: 70: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 70: Potential Energy = 1.5625764e+02 70: Maximum force = 7.5018237e+03 on atom 9 70: Norm of force = 3.6139019e+03 70: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 70: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Reading energy frame 2 time 4.000 Last energy frame read 2 time 4.000 [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (110 ms) 70: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 70: 70: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 70: that with the Verlet scheme, nstlist has no effect on the accuracy of 70: your simulation. 70: 70: 70: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 70: setting nstcomm equal to nstcalcenergy for less overhead 70: 70: 70: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 70: 70: Generated 20503 of the 20503 non-bonded parameter combinations 70: Generating 1-4 interactions: fudge = 1 70: 70: Generated 17396 of the 20503 1-4 parameter combinations 70: 70: Excluding 3 bonded neighbours molecule type 'Glycine' 70: Number of degrees of freedom in T-Coupling group System is 27.00 70: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 70: 70: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: You are using a plain Coulomb cut-off, which might produce artifacts. 70: You might want to consider using PME electrostatics. 70: 70: 70: 70: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 70: COM removal frequency is set to (4). 70: Other settings require a global communication frequency of 100. 70: Note that this will require additional global communication steps, 70: which will reduce performance when using multiple ranks. 70: Consider setting nstcomm to a multiple of 100. 70: 70: 70: There were 4 NOTEs 70: 70: There was 1 WARNING 70: 70: This run will generate roughly 0 Mb of data 70: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (52 ms) 70: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1015 ms total) 70: 70: [----------] Global test environment tear-down 70: [==========] 12 tests from 2 test suites ran. (2963 ms total) 70: [ PASSED ] 12 tests. 70/91 Test #70: Minimize2RankTests ........................... Passed 3.28 sec test 71 Start 71: MdrunNonIntegratorTests 71: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunNonIntegratorTests.xml" 71: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 71: Test timeout computed to be: 600 71: [==========] Running 46 tests from 3 test suites. 71: [----------] Global test environment set-up. 71: [----------] 1 test from NonbondedBenchTest 71: [ RUN ] NonbondedBenchTest.BasicEndToEndTest 71: SIMD width: 4 71: System size: 3000 atoms 71: Cut-off radius: 1 nm 71: Number of threads: 1 71: Number of iterations: 1 71: Compute energies: no 71: Ewald excl. corr.: analytical 71: 71: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle 71: total useful 71: Ewald all geom. 4xM 0.117 0.1166 10.2121 5.4027 71: [ OK ] NonbondedBenchTest.BasicEndToEndTest (14 ms) 71: [----------] 1 test from NonbondedBenchTest (14 ms total) 71: 71: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 71: NVE simulation: will use the initial temperature of 68.810 K for 71: determining the Verlet buffer size 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 16 steps, 0.0 ps. 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.064 0.032 199.5 71: (ns/day) (hour/ns) 71: Performance: 45.552 0.527 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr' 71: 71: trr version: GMX_trn_file (single precision) 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 24 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 189.4 71: (ns/day) (hour/ns) 71: Performance: 4862.347 0.005 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (78 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 71: NVE simulation: will use the initial temperature of 68.810 K for 71: determining the Verlet buffer size 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 16 steps, 0.0 ps. 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.131 0.066 199.9 71: (ns/day) (hour/ns) 71: Performance: 22.351 1.074 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 49 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.034 0.017 199.7 71: (ns/day) (hour/ns) 71: Performance: 87.177 0.275 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (97 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 16 steps, 0.0 ps. 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.713 nm, buffer size 0.013 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.111 0.056 199.9 71: (ns/day) (hour/ns) 71: Performance: 26.383 0.910 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.712 to 0.744 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.038 0.019 199.7 71: (ns/day) (hour/ns) 71: Performance: 77.674 0.309 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (84 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Number of degrees of freedom in T-Coupling group System is 33.00 71: 71: There were 2 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Argon' 71: 16 steps, 0.0 ps. 71: Generated 1 of the 1 non-bonded parameter combinations 71: 71: Excluding 1 bonded neighbours molecule type 'Argon' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.111 0.055 199.8 71: (ns/day) (hour/ns) 71: Performance: 26.509 0.905 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Argon', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.038 0.019 199.7 71: (ns/day) (hour/ns) 71: Performance: 77.678 0.309 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (84 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 71: NVE simulation: will use the initial temperature of 398.997 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 16 steps, 0.0 ps. 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.043 0.022 199.3 71: (ns/day) (hour/ns) 71: Performance: 67.926 0.353 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 31 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.039 0.020 199.6 71: (ns/day) (hour/ns) 71: Performance: 74.293 0.323 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (259 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 71: NVE simulation: will use the initial temperature of 398.997 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 16 steps, 0.0 ps. 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.166 0.083 199.9 71: (ns/day) (hour/ns) 71: Performance: 17.710 1.355 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 43 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.030 0.015 199.6 71: (ns/day) (hour/ns) 71: Performance: 97.351 0.247 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (288 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 16 steps, 0.0 ps. 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.738 nm, buffer size 0.038 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.735 nm, buffer size 0.035 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.127 0.063 199.8 71: (ns/day) (hour/ns) 71: Performance: 23.149 1.037 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 100, rlist from 0.735 to 0.831 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 43 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.038 0.019 199.7 71: (ns/day) (hour/ns) 71: Performance: 76.826 0.312 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (253 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 27.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'spc2' 71: 16 steps, 0.0 ps. 71: Generated 330891 of the 330891 non-bonded parameter combinations 71: 71: Generated 330891 of the 330891 1-4 parameter combinations 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.157 0.078 199.9 71: (ns/day) (hour/ns) 71: Performance: 18.724 1.282 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'spc2', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 37 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.033 0.017 199.6 71: (ns/day) (hour/ns) 71: Performance: 87.860 0.273 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (258 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: NVE simulation: will use the initial temperature of 456.887 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 6 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 16 steps, 0.0 ps. 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.226 0.113 199.9 71: (ns/day) (hour/ns) 71: Performance: 12.963 1.851 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 34 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.060 0.030 199.8 71: (ns/day) (hour/ns) 71: Performance: 49.029 0.490 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (178 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: NVE simulation: will use the initial temperature of 456.887 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 6 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 6 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 16 steps, 0.0 ps. 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.742 nm, buffer size 0.042 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.737 nm, buffer size 0.037 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.011 0.006 197.4 71: (ns/day) (hour/ns) 71: Performance: 261.319 0.092 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 19 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.000 188.6 71: (ns/day) (hour/ns) 71: Performance: 3081.838 0.008 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (22 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 5 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 16 steps, 0.0 ps. 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.538 0.269 200.0 71: (ns/day) (hour/ns) 71: Performance: 5.455 4.400 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 80, rlist from 0.748 to 0.865 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 43 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.065 0.032 199.8 71: (ns/day) (hour/ns) 71: Performance: 45.473 0.528 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (440 ms) 71: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: 71: NOTE 3 [file unknown]: 71: You are using constraints on all bonds, whereas the forcefield has been 71: parametrized only with constraints involving hydrogen atoms. We suggest 71: using constraints = h-bonds instead, this will also improve performance. 71: 71: Number of degrees of freedom in T-Coupling group System is 23.00 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 71: There are 9 non-linear virtual site constructions. Their contribution to 71: the energy error is approximated. In most cases this does not affect the 71: error significantly. 71: 71: 71: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 5 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun 'Alanine dipeptide in vacuo' 71: 16 steps, 0.0 ps. 71: Generated 2145 of the 2145 non-bonded parameter combinations 71: 71: Generated 2145 of the 2145 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 71: 71: turning all bonds into constraints... 71: 71: Cleaning up constraints and constant bonded interactions with virtual sites 71: 71: Removed 18 Angles with virtual sites, 21 left 71: 71: Removed 10 Proper Dih.s with virtual sites, 44 left 71: 71: Converted 15 Constraints with virtual sites to connections, 7 left 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.733 nm, buffer size 0.033 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.729 nm, buffer size 0.029 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.665 0.333 200.0 71: (ns/day) (hour/ns) 71: Performance: 4.413 5.438 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 25, rlist from 0.729 to 0.81 71: 71: Update groups can not be used for this system because an incompatible virtual site type is used 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 61 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.066 0.033 199.8 71: (ns/day) (hour/ns) 71: Performance: 44.781 0.536 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (437 ms) 71: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2484 ms total) 71: 71: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: NOTE: 21 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.424 0.212 199.9 71: (ns/day) (hour/ns) 71: Performance: 6.922 3.467 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.047 0.024 199.6 71: (ns/day) (hour/ns) 71: Performance: 62.476 0.384 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (375 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.174 0.087 199.8 71: (ns/day) (hour/ns) 71: Performance: 16.831 1.426 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.047 0.024 199.6 71: (ns/day) (hour/ns) 71: Performance: 62.214 0.386 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (131 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.175 0.087 199.8 71: (ns/day) (hour/ns) 71: Performance: 16.819 1.427 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.048 0.024 199.6 71: (ns/day) (hour/ns) 71: Performance: 61.365 0.391 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (131 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.175 0.088 199.8 71: (ns/day) (hour/ns) 71: Performance: 16.752 1.433 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 46 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.050 0.025 199.6 71: (ns/day) (hour/ns) 71: Performance: 58.925 0.407 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (135 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.175 0.088 199.8 71: (ns/day) (hour/ns) 71: Performance: 16.762 1.432 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.047 0.024 199.5 71: (ns/day) (hour/ns) 71: Performance: 61.750 0.389 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (132 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.179 0.090 199.8 71: (ns/day) (hour/ns) 71: Performance: 16.387 1.465 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 43 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.052 0.026 199.6 71: (ns/day) (hour/ns) 71: Performance: 56.675 0.423 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (136 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.178 0.089 199.8 71: (ns/day) (hour/ns) 71: Performance: 16.486 1.456 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.047 0.024 199.6 71: (ns/day) (hour/ns) 71: Performance: 62.015 0.387 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (133 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.175 0.088 199.8 71: (ns/day) (hour/ns) 71: Performance: 16.760 1.432 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.047 0.024 199.6 71: (ns/day) (hour/ns) 71: Performance: 61.756 0.389 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (132 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.175 0.087 199.8 71: (ns/day) (hour/ns) 71: Performance: 16.788 1.430 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 44 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.048 0.024 199.6 71: (ns/day) (hour/ns) 71: Performance: 61.646 0.389 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (131 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.059 0.029 199.4 71: (ns/day) (hour/ns) 71: Performance: 49.870 0.481 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 19 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.001 0.001 190.1 71: (ns/day) (hour/ns) 71: Performance: 2442.741 0.010 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (47 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.022 0.011 198.7 71: (ns/day) (hour/ns) 71: Performance: 133.167 0.180 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 41 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.054 0.027 199.6 71: (ns/day) (hour/ns) 71: Performance: 54.395 0.441 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (53 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.461 0.230 200.0 71: (ns/day) (hour/ns) 71: Performance: 6.378 3.763 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 39 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.170 0.085 199.9 71: (ns/day) (hour/ns) 71: Performance: 17.242 1.392 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (371 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.566 0.283 200.0 71: (ns/day) (hour/ns) 71: Performance: 5.188 4.626 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 37 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.114 0.057 199.8 71: (ns/day) (hour/ns) 71: Performance: 25.815 0.930 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (399 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.491 0.246 200.0 71: (ns/day) (hour/ns) 71: Performance: 5.980 4.013 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 34 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.101 0.051 199.8 71: (ns/day) (hour/ns) 71: Performance: 28.961 0.829 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (352 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.353 0.177 199.9 71: (ns/day) (hour/ns) 71: Performance: 8.321 2.884 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 33 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.085 0.043 199.7 71: (ns/day) (hour/ns) 71: Performance: 34.374 0.698 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (259 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.388 0.194 200.0 71: (ns/day) (hour/ns) 71: Performance: 7.563 3.173 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 47 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.081 0.040 199.7 71: (ns/day) (hour/ns) 71: Performance: 36.407 0.659 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (276 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.352 0.176 199.9 71: (ns/day) (hour/ns) 71: Performance: 8.351 2.874 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 39 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.080 0.040 199.7 71: (ns/day) (hour/ns) 71: Performance: 36.451 0.658 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (251 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.354 0.177 199.9 71: (ns/day) (hour/ns) 71: Performance: 8.288 2.896 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 30 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.070 0.035 199.7 71: (ns/day) (hour/ns) 71: Performance: 41.964 0.572 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (242 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.347 0.174 199.9 71: (ns/day) (hour/ns) 71: Performance: 8.456 2.838 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 57 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.061 0.031 199.7 71: (ns/day) (hour/ns) 71: Performance: 47.800 0.502 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (241 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.360 0.180 200.0 71: (ns/day) (hour/ns) 71: Performance: 8.165 2.939 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 33 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.105 0.053 199.8 71: (ns/day) (hour/ns) 71: Performance: 27.817 0.863 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (268 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.471 0.235 200.0 71: (ns/day) (hour/ns) 71: Performance: 6.242 3.845 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 41 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.101 0.051 199.8 71: (ns/day) (hour/ns) 71: Performance: 28.960 0.829 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (331 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 71: NVE simulation: will use the initial temperature of 293.480 K for 71: determining the Verlet buffer size 71: 71: 71: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 4 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.756 nm, buffer size 0.056 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.468 0.234 200.0 71: (ns/day) (hour/ns) 71: Performance: 6.270 3.827 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Can not increase nstlist because an NVE ensemble is used 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 48 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.103 0.052 199.8 71: (ns/day) (hour/ns) 71: Performance: 28.388 0.845 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (334 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.446 0.223 199.9 71: (ns/day) (hour/ns) 71: Performance: 6.591 3.642 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 31 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.110 0.055 199.7 71: (ns/day) (hour/ns) 71: Performance: 26.753 0.897 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (350 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.428 0.214 199.9 71: (ns/day) (hour/ns) 71: Performance: 6.866 3.496 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 49 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.101 0.051 199.8 71: (ns/day) (hour/ns) 71: Performance: 28.980 0.828 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (346 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.445 0.222 199.9 71: (ns/day) (hour/ns) 71: Performance: 6.602 3.635 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 20 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.105 0.053 199.8 71: (ns/day) (hour/ns) 71: Performance: 27.934 0.859 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (350 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.238 0.119 199.9 71: (ns/day) (hour/ns) 71: Performance: 12.356 1.942 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 40 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.054 0.027 199.6 71: (ns/day) (hour/ns) 71: Performance: 54.377 0.441 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (205 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.212 0.106 199.9 71: (ns/day) (hour/ns) 71: Performance: 13.834 1.735 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 41 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.051 0.026 199.6 71: (ns/day) (hour/ns) 71: Performance: 57.030 0.421 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (159 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.223 0.111 199.9 71: (ns/day) (hour/ns) 71: Performance: 13.187 1.820 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 40 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.051 0.026 199.6 71: (ns/day) (hour/ns) 71: Performance: 57.245 0.419 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (164 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.275 0.137 199.9 71: (ns/day) (hour/ns) 71: Performance: 10.689 2.245 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 55 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.071 0.035 199.7 71: (ns/day) (hour/ns) 71: Performance: 41.471 0.579 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (209 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.230 0.115 199.9 71: (ns/day) (hour/ns) 71: Performance: 12.744 1.883 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 27 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.032 0.016 199.5 71: (ns/day) (hour/ns) 71: Performance: 91.654 0.262 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (187 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.046 0.023 199.4 71: (ns/day) (hour/ns) 71: Performance: 63.030 0.381 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 31 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.068 0.034 199.7 71: (ns/day) (hour/ns) 71: Performance: 43.042 0.558 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (92 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.271 0.136 199.9 71: (ns/day) (hour/ns) 71: Performance: 10.824 2.217 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 26 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.080 0.040 199.6 71: (ns/day) (hour/ns) 71: Performance: 36.569 0.656 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (207 ms) 71: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 71: 71: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 71: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 71: that with the Verlet scheme, nstlist has no effect on the accuracy of 71: your simulation. 71: 71: 71: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 71: Setting nstcalcenergy (100) equal to nstenergy (4) 71: 71: Generating 1-4 interactions: fudge = 0.5 71: Number of degrees of freedom in T-Coupling group System is 79.00 71: 71: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 71: You are using a plain Coulomb cut-off, which might produce artifacts. 71: You might want to consider using PME electrostatics. 71: 71: 71: 71: There were 3 NOTEs 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting mdrun '30 system in water' 71: 16 steps, 0.0 ps. 71: Generated 2485 of the 2485 non-bonded parameter combinations 71: 71: Generated 2485 of the 2485 1-4 parameter combinations 71: 71: Excluding 3 bonded neighbours molecule type 'nonanol' 71: 71: turning H bonds into constraints... 71: 71: Excluding 2 bonded neighbours molecule type 'SOL' 71: 71: turning H bonds into constraints... 71: 71: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 71: 71: Calculated rlist for 1x1 atom pair-list as 0.764 nm, buffer size 0.064 nm 71: 71: Set rlist, assuming 4x4 atom pair-list, to 0.757 nm, buffer size 0.057 nm 71: 71: Note that mdrun will redetermine rlist based on the actual pair-list setup 71: 71: This run will generate roughly 0 Mb of data 71: 71: Writing final coordinates. 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.377 0.188 199.9 71: (ns/day) (hour/ns) 71: Performance: 7.792 3.080 71: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 71: Changing nstlist from 8 to 20, rlist from 0.757 to 0.863 71: 71: Using 1 MPI process 71: Using 2 OpenMP threads 71: 71: 71: NOTE: The number of threads is not equal to the number of (logical) cpus 71: and the -pin option is set to auto: will not pin threads to cpus. 71: This can lead to significant performance degradation. 71: Consider using -pin on (and -pinoffset in case you run multiple jobs). 71: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr' 71: 71: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 71: 71: NOTE: 22 % of the run time was spent in pair search, 71: you might want to increase nstlist (this has no effect on accuracy) 71: 71: Core t (s) Wall t (s) (%) 71: Time: 0.094 0.047 199.8 71: (ns/day) (hour/ns) 71: Performance: 31.210 0.769 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file 71: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file 71: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 71: 71: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (288 ms) 71: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (7436 ms total) 71: 71: [----------] Global test environment tear-down 71: [==========] 46 tests from 3 test suites ran. (9948 ms total) 71: [ PASSED ] 46 tests. 71/91 Test #71: MdrunNonIntegratorTests ...................... Passed 10.25 sec test 72 Start 72: MdrunTpiTests 72: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-tpi-test "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunTpiTests.xml" 72: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 72: Test timeout computed to be: 600 72: [==========] Running 2 tests from 1 test suite. 72: [----------] Global test environment set-up. 72: [----------] 2 tests from Simple/TpiTest 72: [ RUN ] Simple/TpiTest.ReproducesOutput/0 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 1308.00 72: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 72: TPI is not implemented for GPUs. 72: 72: Using 1 MPI process 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: Reading frames from gro file '216 water molecules', 648 atoms. 72: Reading frame 0 time 0.000 mu 6.291e+01 6.291e+01 72: Last frame 0 time 0.000 72: Generated 331705 of the 331705 non-bonded parameter combinations 72: 72: Generated 331705 of the 331705 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Excluding 3 bonded neighbours molecule type 'methane' 72: Analysing residue names: 72: There are: 216 Water residues 72: There are: 1 Other residues 72: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] Simple/TpiTest.ReproducesOutput/0 (317 ms) 72: [ RUN ] Simple/TpiTest.ReproducesOutput/1 72: Generating 1-4 interactions: fudge = 0.5 72: Number of degrees of freedom in T-Coupling group System is 1308.00 72: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 72: TPI is not implemented for GPUs. 72: 72: Using 1 MPI process 72: Using 1 OpenMP thread 72: 72: 72: NOTE: Thread affinity was not set. 72: Reading frames from gro file '216 water molecules', 648 atoms. 72: Reading frame 0 time 0.000 mu 4.535e+01 4.535e+01 72: Last frame 0 time 0.000 72: Generated 331705 of the 331705 non-bonded parameter combinations 72: 72: Generated 331705 of the 331705 1-4 parameter combinations 72: 72: Excluding 2 bonded neighbours molecule type 'SOL' 72: 72: Excluding 3 bonded neighbours molecule type 'methane' 72: Analysing residue names: 72: There are: 216 Water residues 72: There are: 1 Other residues 72: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 72: 72: This run will generate roughly 0 Mb of data 72: [ OK ] Simple/TpiTest.ReproducesOutput/1 (397 ms) 72: [----------] 2 tests from Simple/TpiTest (715 ms total) 72: 72: [----------] Global test environment tear-down 72: [==========] 2 tests from 1 test suite ran. (719 ms total) 72: [ PASSED ] 2 tests. 72/91 Test #72: MdrunTpiTests ................................ Passed 0.87 sec test 73 Start 73: MdrunMpiTests 73: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-mpi-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMpiTests.xml" 73: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 73: Test timeout computed to be: 600 73: [==========] Running 16 tests from 2 test suites. 73: [----------] Global test environment set-up. 73: [----------] 4 tests from MimicTest 73: [ RUN ] MimicTest.OneQuantumMol 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Setting the LD random seed to -1409696775 73: 73: Generated 10 of the 10 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 10 of the 10 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group rest is 21.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 73: 73: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 73: Reading frame 0 time 0.000 Last frame 0 time 0.000 73: 73: NOTE: 38 % of the run time was spent in domain decomposition, 73: 4 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: NOTE: 33 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.211 0.065 326.1 73: (ns/day) (hour/ns) 73: Performance: 1.337 17.955 73: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.OneQuantumMol (200 ms) 73: [ RUN ] MimicTest.AllQuantumMol 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Setting the LD random seed to 2142732222 73: 73: Generated 10 of the 10 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 10 of the 10 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group rest is 21.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 73: 73: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 73: Reading frame 0 time 0.000 Last frame 0 time 0.000 73: 73: NOTE: 6 % of the run time was spent in domain decomposition, 73: 12 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: NOTE: 32 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.201 0.057 350.4 73: (ns/day) (hour/ns) 73: Performance: 1.509 15.900 73: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.AllQuantumMol (110 ms) 73: [ RUN ] MimicTest.TwoQuantumMol 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: Setting the LD random seed to 1039905726 73: 73: Generated 10 of the 10 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 10 of the 10 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: 73: This run will generate roughly 0 Mb of data 73: Number of degrees of freedom in T-Coupling group rest is 21.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/4water.gro' 73: 73: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 73: Reading frame 0 time 0.000 Last frame 0 time 0.000 73: 73: NOTE: 49 % of the run time was spent in domain decomposition, 73: 4 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: NOTE: 15 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.216 0.054 399.8 73: (ns/day) (hour/ns) 73: Performance: 1.602 14.979 73: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 73: For a correct single-point energy evaluation with nsteps = 0, use 73: continuation = yes to avoid constraining the input coordinates. 73: 73: [ OK ] MimicTest.TwoQuantumMol (128 ms) 73: [ RUN ] MimicTest.BondCuts 73: Setting the LD random seed to -1493222155 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 2211 of the 2211 non-bonded parameter combinations 73: 73: Generated 2211 of the 2211 1-4 parameter combinations 73: 73: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 73: Number of degrees of freedom in T-Coupling group rest is 66.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 73: NVE simulation: will use the initial temperature of 300.368 K for 73: determining the Verlet buffer size 73: 73: 73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 73: 73: Calculated rlist for 1x1 atom pair-list as 1.048 nm, buffer size 0.048 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 1.036 nm, buffer size 0.036 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 73: You are using a plain Coulomb cut-off, which might produce artifacts. 73: You might want to consider using PME electrostatics. 73: 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: There were 3 NOTEs 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/ala.gro' 73: 73: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 73: Reading frame 0 time 0.000 Last frame 0 time 0.000 73: 73: NOTE: 34 % of the run time was spent in domain decomposition, 73: 12 % of the run time was spent in pair search, 73: you might want to increase nstlist (this has no effect on accuracy) 73: 73: NOTE: 31 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 0.166 0.042 392.7 73: (ns/day) (hour/ns) 73: Performance: 2.044 11.743 73: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 73: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] MimicTest.BondCuts (161 ms) 73: [----------] 4 tests from MimicTest (617 ms total) 73: 73: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest 73: Setting the LD random seed to -1208179362 73: 73: Generated 3 of the 3 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 3 of the 3 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group rest is 9.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: There was 1 NOTE 73: Setting the LD random seed to -1079066793 73: 73: Generated 3 of the 3 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 3 of the 3 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group System is 9.00 73: 73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 73: 73: Calculated rlist for 1x1 atom pair-list as 1.017 nm, buffer size 0.017 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 1.005 nm, buffer size 0.005 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: 73: This run will generate roughly 0 Mb of data 73: Setting the LD random seed to 1866167807 73: 73: Generated 3 of the 3 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 3 of the 3 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group rest is 9.00 73: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 73: 73: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 73: NVE simulation with an initial temperature of zero: will use a Verlet 73: buffer of 10%. Check your energy drift! 73: 73: Calculating fourier grid dimensions for X Y Z 73: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 73: 73: Estimate for the relative computational load of the PME mesh part: 1.00 73: 73: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 73: The optimal PME mesh load for parallel simulations is below 0.5 73: and for highly parallel simulations between 0.25 and 0.33, 73: for higher performance, increase the cut-off and the PME grid spacing. 73: 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: There were 2 NOTEs 73: Setting the LD random seed to -92342547 73: 73: Generated 3 of the 3 non-bonded parameter combinations 73: Generating 1-4 interactions: fudge = 0.5 73: 73: Generated 3 of the 3 1-4 parameter combinations 73: 73: Excluding 2 bonded neighbours molecule type 'SOL' 73: Number of degrees of freedom in T-Coupling group System is 9.00 73: 73: The largest distance between excluded atoms is 0.164 nm between atom 2 and 3 73: 73: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 73: 73: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 73: 73: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 73: 73: Note that mdrun will redetermine rlist based on the actual pair-list setup 73: Calculating fourier grid dimensions for X Y Z 73: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 73: 73: Estimate for the relative computational load of the PME mesh part: 1.00 73: 73: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_input.mdp]: 73: The optimal PME mesh load for parallel simulations is below 0.5 73: and for highly parallel simulations between 0.25 and 0.33, 73: for higher performance, increase the cut-off and the PME grid spacing. 73: 73: 73: 73: This run will generate roughly 0 Mb of data 73: 73: There was 1 NOTE 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was turned on during the run due to measured imbalance. 73: Average load imbalance: 15.8%. 73: The balanceable part of the MD step is 61%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 9.6%. 73: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 73: 73: NOTE: 9.6 % of the available CPU time was lost due to load imbalance 73: in the domain decomposition. 73: You can consider manually changing the decomposition (option -dd); 73: e.g. by using fewer domains along the box dimension in which there is 73: considerable inhomogeneity in the simulated system. 73: 73: NOTE: 8 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 1.446 0.373 387.6 73: (ns/day) (hour/ns) 73: Performance: 4.863 4.935 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (498 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_RF_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Changing nstlist from 10 to 50, rlist from 1.005 to 1.136 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: NOTE: 11 % of the run time was spent communicating energies, 73: you might want to increase some nst* mdp options 73: 73: Core t (s) Wall t (s) (%) 73: Time: 1.670 0.431 387.1 73: (ns/day) (hour/ns) 73: Performance: 4.206 5.706 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (486 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: 73: Dynamic load balancing report: 73: DLB was off during the run due to low measured imbalance. 73: Average load imbalance: 2.0%. 73: The balanceable part of the MD step is 30%, load imbalance is computed from this. 73: Part of the total run time spent waiting due to load imbalance: 0.6%. 73: 73: 73: Core t (s) Wall t (s) (%) 73: Time: 1.055 0.264 399.9 73: (ns/day) (hour/ns) 73: Performance: 6.876 3.491 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme0 (20865 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_No.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Can not increase nstlist because an NVE ensemble is used 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 2.130 0.536 397.3 73: (ns/day) (hour/ns) 73: Performance: 3.385 7.090 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme1 (12344 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 (3 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Changing nstlist from 10 to 100, rlist from 1 to 1 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 4.136 1.040 397.8 73: (ns/day) (hour/ns) 73: Performance: 1.745 13.755 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme0 (1181 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 73: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/DomainDecomposition_DomDecSpecialCasesTest_PME_TemperatureAndPressure.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 73: Changing nstlist from 10 to 100, rlist from 1 to 1 73: 73: Using 2 MPI processes 73: Using 2 OpenMP threads per MPI process 73: 73: 73: NOTE: The number of threads is not equal to the number of (logical) cpus 73: and the -pin option is set to auto: will not pin threads to cpus. 73: This can lead to significant performance degradation. 73: Consider using -pin on (and -pinoffset in case you run multiple jobs). 73: starting mdrun 'spc2' 73: 20 steps, 0.0 ps. 73: 73: Writing final coordinates. 73: 73: Core t (s) Wall t (s) (%) 73: Time: 3.625 0.918 395.0 73: (ns/day) (hour/ns) 73: Performance: 1.977 12.142 73: [ OK ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 (1254 ms) 73: [ RUN ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 (0 ms) 73: [----------] 12 tests from DomainDecomposition/DomDecSpecialCasesTest (36698 ms total) 73: 73: [----------] Global test environment tear-down 73: [==========] 16 tests from 2 test suites ran. (37470 ms total) 73: [ PASSED ] 10 tests. 73: [ SKIPPED ] 6 tests, listed below: 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme1 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_No_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme1 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/RF_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_No_coupling_nbcpu_pmecpu_updatecpu_npme2 73: [ SKIPPED ] DomainDecomposition/DomDecSpecialCasesTest.EmptyDomain/PME_TemperatureAndPressure_coupling_nbcpu_pmecpu_updatecpu_npme2 73/91 Test #73: MdrunMpiTests ................................ Passed 37.95 sec test 74 Start 74: MdrunMultiSimTests 74: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-multisim-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMultiSimTests.xml" 74: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 74: Test timeout computed to be: 600 74: [==========] Running 6 tests from 2 test suites. 74: [----------] Global test environment set-up. 74: [----------] 4 tests from InNvt/MultiSimTest 74: [ RUN ] InNvt/MultiSimTest.ExitsNormally/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to 1811765243 74: Setting the LD random seed to -1176546561 74: Setting the LD random seed to -402936129 74: Generating 1-4 interactions: fudge = 0.5 74: 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -487237172 74: 74: Velocities were taken from a Maxwell distribution at 268 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 NOTEs 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -42033169 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 NOTEs 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1415815235 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to -65737 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -205537348 74: 74: Velocities were taken from a Maxwell distribution at 288 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 2 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 0 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 1 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 3 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: [ OK ] InNvt/MultiSimTest.ExitsNormally/0 (448 ms) 74: [ RUN ] InNvt/MultiSimTest.ExitsNormally/1 74: Setting the LD random seed to -121903623 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -578818116 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -10486546 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1243712644 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 0 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: This is simulation 1 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: Writing final coordinates. 74: 74: NOTE: 10 % of the run time was spent in domain decomposition, 74: 4 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 28 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Writing final coordinates. 74: 74: NOTE: 50 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: [ OK ] InNvt/MultiSimTest.ExitsNormally/1 (475 ms) 74: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimT 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Setting the LD random seed to -3156993 74: Setting the LD random seed to -179336258 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Setting gen_seed to -67119367 74: 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Setting gen_seed to -1077936129 74: est_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Setting the LD random seed to 1062420207 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1056849 74: 74: Velocities were taken from a Maxwell distribution at 288 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -289423378 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to 2130657279 74: 74: Velocities were taken from a Maxwell distribution at 268 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 2 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 2 steps, 0.0 ps. 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 1 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 1 steps, 0.0 ps. 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 0 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 0 steps, 0.0 ps. 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: NOTE: 17 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: For a correct single-point energy evaluation with nsteps = 0, use 74: continuation = yes to avoid constraining the input coordinates. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 3 NOTEs 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 3 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps. 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/0 (129 ms) 74: [ RUN ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 74: Setting the LD random seed to 1979710447 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to 2105191326 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Setting the LD random seed to -558895119 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -50602051 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTest_ExitsNormallyWithDifferentNumbersOfStepsPerSimulation_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: This is simulation 1 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: This is simulation 0 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 1 steps, 0.0 ps. 74: starting mdrun 'spc2' 74: 0 steps, 0.0 ps. 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Note: The number of steps is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: 74: NOTE: 53 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 73 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: [ OK ] InNvt/MultiSimTest.ExitsNormallyWithDifferentNumbersOfStepsPerSimulation/1 (417 ms) 74: [----------] 4 tests from InNvt/MultiSimTest (1564 ms total) 74: 74: [----------] 2 tests from InNvt/MultiSimTerminationTest 74: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to -369625409 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1077936165 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: This run will generate roughly 0 Mb of data 74: 74: There were 2 NOTEs 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Setting the LD random seed to 2147344383 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -307654 74: 74: Velocities were taken from a Maxwell distribution at 268 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to -948200194 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: Generating 1-4 interactions: fudge = 0.5 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1157972355 74: 74: Velocities were taken from a Maxwell distribution at 288 K 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: This run will generate roughly 0 Mb of data 74: Setting the LD random seed to -9553317 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -1158086666 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: There were 2 NOTEs 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: This is simulation 2 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 0 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 1 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: This is simulation 3 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: 74: This is simulation 0 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: 74: This is simulation 2 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: 74: This is simulation 1 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: 74: This is simulation 3 out of 4 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 1 MPI process 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: Using 1 OpenMP thread 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: 74: Writing final coordinates. 74: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (780 ms) 74: [ RUN ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: 74: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 74: You have set rlist larger than the interaction cut-off, but you also have 74: verlet-buffer-tolerance > 0. Will set rlist using 74: verlet-buffer-tolerance. 74: 74: Setting the LD random seed to 1236497342 74: Setting the LD random seed to -1645224985 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: Generating 1-4 interactions: fudge = 0.5 74: Number of degrees of freedom in T-Coupling group System is 9.00 74: 74: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1_input.mdp]: 74: You are using a plain Coulomb cut-off, which might produce artifacts. 74: You might want to consider using PME electrostatics. 74: 74: 74: 74: There were 2 NOTEs 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to -444615683 74: 74: Velocities were taken from a Maxwell distribution at 298 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: 74: Generated 3 of the 3 non-bonded parameter combinations 74: 74: Generated 3 of the 3 1-4 parameter combinations 74: 74: Excluding 2 bonded neighbours molecule type 'SOL' 74: 74: Setting gen_seed to 1056436559 74: 74: Velocities were taken from a Maxwell distribution at 278 K 74: 74: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 74: 74: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 74: 74: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 74: 74: Note that mdrun will redetermine rlist based on the actual pair-list setup 74: 74: This run will generate roughly 0 Mb of data 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 74: 74: This is simulation 0 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: This is simulation 1 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 100 steps, 0.1 ps. 74: 74: Step 3: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 5.2%. 74: The balanceable part of the MD step is 6%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 0.3%. 74: 74: 74: NOTE: 24 % of the run time was spent in domain decomposition, 74: 5 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: 74: NOTE: 24 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 74: 74: 74: Dynamic load balancing report: 74: DLB was off during the run due to low measured imbalance. 74: Average load imbalance: 18.8%. 74: The balanceable part of the MD step is 0%, load imbalance is computed from this. 74: Part of the total run time spent waiting due to load imbalance: 0.0%. 74: 74: 74: NOTE: 55 % of the run time was spent in domain decomposition, 74: 0 % of the run time was spent in pair search, 74: you might want to increase nstlist (this has no effect on accuracy) 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: 74: This is simulation 0 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps). 74: 74: Note: The initial step is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_MultiSimTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 74: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 74: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 74: 74: 74: This is simulation 1 out of 2 running as a composite GROMACS 74: multi-simulation job. Setup for this simulation: 74: 74: Using 2 MPI processes 74: Using 1 OpenMP thread per MPI process 74: 74: 74: NOTE: The number of threads is not equal to the number of (logical) cpus 74: and the -pin option is set to auto: will not pin threads to cpus. 74: This can lead to significant performance degradation. 74: Consider using -pin on (and -pinoffset in case you run multiple jobs). 74: starting mdrun 'spc2' 74: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 74: 74: Note: The initial step is not consistent across multi simulations, 74: but we are proceeding anyway! 74: 74: Writing final coordinates. 74: 74: NOTE: 37 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: 74: NOTE: 37 % of the run time was spent communicating energies, 74: you might want to increase some nst* mdp options 74: [ OK ] InNvt/MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/1 (760 ms) 74: [----------] 2 tests from InNvt/MultiSimTerminationTest (1588 ms total) 74: 74: [----------] Global test environment tear-down 74: [==========] 6 tests from 2 test suites ran. (3279 ms total) 74: [ PASSED ] 6 tests. 74/91 Test #74: MdrunMultiSimTests ........................... Passed 3.79 sec test 75 Start 75: MdrunMultiSimReplexTests 75: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-multisim-replex-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMultiSimReplexTests.xml" 75: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 75: Test timeout computed to be: 600 75: [==========] Running 5 tests from 2 test suites. 75: [----------] Global test environment set-up. 75: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest 75: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Setting the LD random seed to -1166147877 75: Setting the LD random seed to 2134041331 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Setting the LD random seed to -541861938 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Generating 1-4 interactions: fudge = 0.5 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Setting the LD random seed to -269717507 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to 1609424894 75: 75: Velocities were taken from a Maxwell distribution at 268 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to 2105079803 75: 75: Velocities were taken from a Maxwell distribution at 288 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -272859142 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -285474850 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: This is simulation 0 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 1 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 2 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 3 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/0 (640 ms) 75: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Setting the LD random seed to -1494231045 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: Setting the LD random seed to -4194313 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -67371393 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Setting gen_seed to -2228233 75: 75: Velocities were taken from a Maxwell distribution at 268 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Setting the LD random seed to -84155941 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Setting the LD random seed to -1881310293 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -39321603 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -370155529 75: 75: Velocities were taken from a Maxwell distribution at 288 K 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: This is simulation 2 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 0 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 1 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: This is simulation 3 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/1 (547 ms) 75: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Setting the LD random seed to -59327329 75: Setting the LD random seed to -1084242659 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -101513 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to 1037928447 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: This is simulation 1 out of 2 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 2 MPI processes 75: This is simulation 0 out of 2 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 2 MPI processes 75: Using 1 OpenMP thread per MPI process 75: 75: Using 1 OpenMP thread per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.3%. 75: The balanceable part of the MD step is 0%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.0%. 75: 75: 75: NOTE: 45 % of the run time was spent in domain decomposition, 75: 0 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: NOTE: 19 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.0%. 75: The balanceable part of the MD step is 0%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.0%. 75: 75: 75: NOTE: 50 % of the run time was spent in domain decomposition, 75: 0 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: NOTE: 16 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: The Berendsen barostat does not generate any strictly correct ensemble, 75: and should not be used for new production simulations (in our opinion). 75: We recommend using the C-rescale barostat instead. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/2 (617 ms) 75: [ RUN ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 75: Setting the LD random seed to -856752145 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -12716041 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to -16860305 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -1090562273 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: There was 1 WARNING 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/WithDifferentControlVariables_ReplicaExchangeEnsembleTest_ExitsNormally_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: This is simulation 1 out of 2 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 2 MPI processes 75: This is simulation 0 out of 2 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 2 MPI processes 75: Using 1 OpenMP thread per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 0.2%. 75: The balanceable part of the MD step is 14%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.0%. 75: 75: 75: NOTE: 12 % of the run time was spent in domain decomposition, 75: 4 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: Using 1 OpenMP thread per MPI process 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 2 steps, 0.0 ps. 75: 75: Writing final coordinates. 75: 75: 75: Dynamic load balancing report: 75: DLB was off during the run due to low measured imbalance. 75: Average load imbalance: 1.0%. 75: The balanceable part of the MD step is 14%, load imbalance is computed from this. 75: Part of the total run time spent waiting due to load imbalance: 0.1%. 75: 75: 75: NOTE: 12 % of the run time was spent in domain decomposition, 75: 4 % of the run time was spent in pair search, 75: you might want to increase nstlist (this has no effect on accuracy) 75: 75: NOTE: 29 % of the run time was spent communicating energies, 75: you might want to increase some nst* mdp options 75: [ OK ] WithDifferentControlVariables/ReplicaExchangeEnsembleTest.ExitsNormally/3 (149 ms) 75: [----------] 4 tests from WithDifferentControlVariables/ReplicaExchangeEnsembleTest (1989 ms total) 75: 75: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest 75: [ RUN ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Setting the LD random seed to -822088738 75: Setting the LD random seed to 801731381 75: Generating 1-4 interactions: fudge = 0.5 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -25165835 75: 75: Velocities were taken from a Maxwell distribution at 288 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: 75: Setting gen_seed to -54542595 75: 75: Velocities were taken from a Maxwell distribution at 298 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: This run will generate roughly 0 Mb of data 75: Setting the LD random seed to 2008992731 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to -335843537 75: 75: Velocities were taken from a Maxwell distribution at 268 K 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: Setting the LD random seed to -1644370945 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: There were 2 NOTEs 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: Generating 1-4 interactions: fudge = 0.5 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You have set rlist larger than the interaction cut-off, but you also have 75: verlet-buffer-tolerance > 0. Will set rlist using 75: verlet-buffer-tolerance. 75: 75: 75: Generated 3 of the 3 non-bonded parameter combinations 75: Generating 1-4 interactions: fudge = 0.5 75: 75: Generated 3 of the 3 1-4 parameter combinations 75: 75: Excluding 2 bonded neighbours molecule type 'SOL' 75: 75: Setting gen_seed to 2132713211 75: 75: Velocities were taken from a Maxwell distribution at 278 K 75: Number of degrees of freedom in T-Coupling group System is 9.00 75: 75: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 75: 75: Calculated rlist for 1x1 atom pair-list as 0.744 nm, buffer size 0.044 nm 75: 75: Set rlist, assuming 4x4 atom pair-list, to 0.736 nm, buffer size 0.036 nm 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 NOTEs 75: Note that mdrun will redetermine rlist based on the actual pair-list setup 75: 75: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0_input.mdp]: 75: You are using a plain Coulomb cut-off, which might produce artifacts. 75: You might want to consider using PME electrostatics. 75: 75: 75: 75: This run will generate roughly 0 Mb of data 75: 75: There were 2 NOTEs 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 75: 75: This is simulation 3 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 100 steps, 0.1 ps. 75: 75: Step 7: Run time exceeded 0.000 hours, will terminate the run within 400 steps 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 75: 75: This is simulation 2 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 100 steps, 0.1 ps. 75: 75: Step 7: Run time exceeded 0.000 hours, will terminate the run within 400 steps 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 75: 75: This is simulation 0 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 100 steps, 0.1 ps. 75: 75: Step 7: Run time exceeded 0.000 hours, will terminate the run within 400 steps 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Changing nstlist from 10 to 1, rlist from 0.736 to 0.7 75: 75: This is simulation 1 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 100 steps, 0.1 ps. 75: 75: Step 7: Run time exceeded 0.000 hours, will terminate the run within 400 steps 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: 75: Writing final coordinates. 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/InNvt_ReplicaExchangeTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 75: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 75: Changing nstlist from 10 to 25, rlist from 0.738 to 0.815 75: 75: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 75: Changing nstlist from 10 to 25, rlist from 0.738 to 0.815 75: 75: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 75: Changing nstlist from 10 to 25, rlist from 0.736 to 0.811 75: 75: 75: This is simulation 0 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: 75: This is simulation 3 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: 75: This is simulation 1 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: 75: This is simulation 2 out of 4 running as a composite GROMACS 75: multi-simulation job. Setup for this simulation: 75: 75: Using 1 MPI process 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: Using 1 OpenMP thread 75: 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: 75: NOTE: The number of threads is not equal to the number of (logical) cpus 75: and the -pin option is set to auto: will not pin threads to cpus. 75: This can lead to significant performance degradation. 75: Consider using -pin on (and -pinoffset in case you run multiple jobs). 75: starting mdrun 'spc2' 75: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 75: 75: Writing final coordinates. 75: starting mdrun 'spc2' 75: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 75: 75: Writing final coordinates. 75: starting mdrun 'spc2' 75: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 75: 75: Writing final coordinates. 75: starting mdrun 'spc2' 75: 102 steps, 0.1 ps (continuing from step 100, 0.1 ps). 75: 75: Writing final coordinates. 75: [ OK ] InNvt/ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts/0 (629 ms) 75: [----------] 1 test from InNvt/ReplicaExchangeTerminationTest (633 ms total) 75: 75: [----------] Global test environment tear-down 75: [==========] 5 tests from 2 test suites ran. (2756 ms total) 75: [ PASSED ] 5 tests. 75/91 Test #75: MdrunMultiSimReplexTests ..................... Passed 3.32 sec test 76 Start 76: MdrunMultiSimReplexEquivalenceTests 76: Test command: /usr/bin/mpiexec "-n" "4" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-multisim-replex-equivalence-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMultiSimReplexEquivalenceTests.xml" 76: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 76: Test timeout computed to be: 600 76: [==========] Running 10 tests from 2 test suites. 76: [----------] Global test environment set-up. 76: [----------] 8 tests from LF/ReplicaExchangeTest 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: This run will generate roughly 0 Mb of data 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 trr version: GMX_trn_file (single precision) 76: 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_1RanksPerSim_s (1492 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSim_s (1504 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread Using 1 OpenMP thread 76: 76: 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_1RanksPerSim_s (1673 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSim_s (1880 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 0.7%. 76: The balanceable part of the MD step is 0%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.0%. 76: 76: 76: NOTE: 23 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 0.5%. 76: The balanceable part of the MD step is 2%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.0%. 76: 76: 76: NOTE: 53 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_Crescale_4Ranks_2RanksPerSim_s (1222 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: There was 1 WARNING 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.2%. 76: The balanceable part of the MD step is 2%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.0%. 76: 76: 76: NOTE: 35 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 0.7%. 76: The balanceable part of the MD step is 38%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.2%. 76: 76: 76: NOTE: 43 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSim_s (905 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 0.4%. 76: The balanceable part of the MD step is 47%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.2%. 76: 76: 76: NOTE: 12 % of the run time was spent in domain decomposition, 76: 3 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 6 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.3%. 76: The balanceable part of the MD step is 48%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.6%. 76: 76: 76: NOTE: 12 % of the run time was spent in domain decomposition, 76: 3 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 6 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_Crescale_4Ranks_2RanksPerSim_s (946 ms) 76: [ RUN ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 76: 1 76: 76: 76: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are generating velocities so I am assuming you are equilibrating a 76: system. You are using Parrinello-Rahman pressure coupling, but this can 76: be unstable for equilibration. If your system crashes, try equilibrating 76: first with Berendsen pressure coupling. If you are not equilibrating the 76: system, you can probably ignore this warning. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 3 NOTEs 76: 76: There was 1 WARNING 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 95.3%. 76: The balanceable part of the MD step is 2%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.9%. 76: 76: 76: NOTE: 24 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 4.6%. 76: The balanceable part of the MD step is 34%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 1.6%. 76: 76: 76: NOTE: 31 % of the run time was spent in domain decomposition, 76: 0 % of the run time was spent in pair search, 76: you might want to increase nstlist (this has no effect on accuracy) 76: 76: NOTE: 24 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/LF_ReplicaExchangeTest_Works_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] LF/ReplicaExchangeTest.Works/md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSim_s (3692 ms) 76: [----------] 8 tests from LF/ReplicaExchangeTest (13564 ms total) 76: 76: [----------] 2 tests from VV/ReplicaExchangeTest 76: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 268 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 288 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: This is simulation 3 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: This is simulation 1 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: This is simulation 2 out of 4 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 1 MPI process 76: Using 1 OpenMP thread 76: 76: Using 1 OpenMP thread 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_2/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_3/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_1RanksPerSim_s (2228 ms) 76: [ RUN ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: 76: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 76: You have set rlist larger than the interaction cut-off, but you also have 76: verlet-buffer-tolerance > 0. Will set rlist using 76: verlet-buffer-tolerance. 76: 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: Generated 330891 of the 330891 non-bonded parameter combinations 76: Generating 1-4 interactions: fudge = 0.5 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 278 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: This run will generate roughly 0 Mb of data 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: There were 2 NOTEs 76: 76: Generated 330891 of the 330891 1-4 parameter combinations 76: 76: Excluding 2 bonded neighbours molecule type 'SOL' 76: 76: Velocities were taken from a Maxwell distribution at 298 K 76: Number of degrees of freedom in T-Coupling group System is 27.00 76: 76: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 76: 76: Calculated rlist for 1x1 atom pair-list as 0.750 nm, buffer size 0.050 nm 76: 76: Set rlist, assuming 4x4 atom pair-list, to 0.741 nm, buffer size 0.041 nm 76: 76: Note that mdrun will redetermine rlist based on the actual pair-list setup 76: 76: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s_input.mdp]: 76: You are using a plain Coulomb cut-off, which might produce artifacts. 76: You might want to consider using PME electrostatics. 76: 76: 76: 76: This run will generate roughly 0 Mb of data 76: 76: There were 2 NOTEs 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: Changing nstlist from 10 to 25, rlist from 0.741 to 0.823 76: 76: This is simulation 0 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: This is simulation 1 out of 2 running as a composite GROMACS 76: multi-simulation job. Setup for this simulation: 76: 76: Using 2 MPI processes 76: Using 1 OpenMP thread per MPI process 76: 76: Using 1 OpenMP thread per MPI process 76: 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: 76: NOTE: The number of threads is not equal to the number of (logical) cpus 76: and the -pin option is set to auto: will not pin threads to cpus. 76: This can lead to significant performance degradation. 76: Consider using -pin on (and -pinoffset in case you run multiple jobs). 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: starting mdrun 'spc2' 76: 16 steps, 0.0 ps. 76: 76: Writing final coordinates. 76: 76: Writing final coordinates. 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.1%. 76: The balanceable part of the MD step is 34%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.4%. 76: 76: 76: NOTE: 49 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: 76: 76: Dynamic load balancing report: 76: DLB was off during the run due to low measured imbalance. 76: Average load imbalance: 1.0%. 76: The balanceable part of the MD step is 34%, load imbalance is computed from this. 76: Part of the total run time spent waiting due to load imbalance: 0.3%. 76: 76: 76: NOTE: 50 % of the run time was spent communicating energies, 76: you might want to increase some nst* mdp options 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_0/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/sim_1/VV_ReplicaExchangeTest_Works_mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s.edr as single precision energy file 76: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 76: [ OK ] VV/ReplicaExchangeTest.Works/mdvv_NoseHoover_No_4Ranks_2RanksPerSim_s (1626 ms) 76: [----------] 2 tests from VV/ReplicaExchangeTest (3931 ms total) 76: 76: [----------] Global test environment tear-down 76: [==========] 10 tests from 2 test suites ran. (17775 ms total) 76: [ PASSED ] 10 tests. 76/91 Test #76: MdrunMultiSimReplexEquivalenceTests .......... Passed 18.24 sec test 77 Start 77: MdrunMpi1RankPmeTests 77: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMpi1RankPmeTests.xml" 77: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 77: Test timeout computed to be: 600 77: [==========] Running 19 tests from 1 test suite. 77: [----------] Global test environment set-up. 77: [----------] 19 tests from ReproducesEnergies/PmeTest 77: Setting the LD random seed to -67442867 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: Number of degrees of freedom in T-Coupling group rest is 12.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: NVE simulation: will use the initial temperature of 1046.791 K for 77: determining the Verlet buffer size 77: 77: Calculating fourier grid dimensions for X Y Z 77: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 77: 77: Estimate for the relative computational load of the PME mesh part: 1.00 77: 77: This run will generate roughly 0 Mb of data 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: The optimal PME mesh load for parallel simulations is below 0.5 77: and for highly parallel simulations between 0.25 and 0.33, 77: for higher performance, increase the cut-off and the PME grid spacing. 77: 77: 77: 77: There were 2 NOTEs 77: 77: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: For a correct single-point energy evaluation with nsteps = 0, use 77: continuation = yes to avoid constraining the input coordinates. 77: 77: Setting the LD random seed to -1094750988 77: 77: Generated 8 of the 10 non-bonded parameter combinations 77: 77: Excluding 2 bonded neighbours molecule type 'Methanol' 77: 77: Excluding 2 bonded neighbours molecule type 'SOL' 77: 77: Searching the wall atom type(s) 77: 77: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 77: 77: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 77: 77: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 77: 77: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 77: 77: Note that mdrun will redetermine rlist based on the actual pair-list setup 77: Calculating fourier grid dimensions for X Y Z 77: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 77: 77: Estimate for the relative computational load of the PME mesh part: 1.00 77: 77: This run will generate roughly 0 Mb of data 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 77: Number of degrees of freedom in T-Coupling group rest is 13.00 77: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 77: 77: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: NVE simulation: will use the initial temperature of 966.268 K for 77: determining the Verlet buffer size 77: 77: 77: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 77: The optimal PME mesh load for parallel simulations is below 0.5 77: and for highly parallel simulations between 0.25 and 0.33, 77: for higher performance, increase the cut-off and the PME grid spacing. 77: 77: 77: 77: There were 3 NOTEs 77: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI process 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 20 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.851 0.425 200.0 77: (ns/day) (hour/ns) 77: Performance: 4.266 5.626 77: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI process 77: Using 2 OpenMP threads 77: 77: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (40773 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 20 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.837 0.419 200.0 77: (ns/day) (hour/ns) 77: Performance: 4.334 5.537 77: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI process 77: Using 2 OpenMP threads 77: 77: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (453 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 0 steps, 0.0 ps. 77: 77: NOTE: 24 % of the run time was spent in domain decomposition, 77: 5 % of the run time was spent in pair search, 77: you might want to increase nstlist (this has no effect on accuracy) 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.042 0.021 199.4 77: (ns/day) (hour/ns) 77: Performance: 4.127 5.816 77: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (110135 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets using PME rank(s) but the simulation is using only one rank 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 77: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 77: Can not increase nstlist because an NVE ensemble is used 77: Using 1 MPI process 77: Using 2 OpenMP threads 77: 77: 77: NOTE: The number of threads is not equal to the number of (logical) cpus 77: and the -pin option is set to auto: will not pin threads to cpus. 77: This can lead to significant performance degradation. 77: Consider using -pin on (and -pinoffset in case you run multiple jobs). 77: starting mdrun 'spc-and-methanol' 77: 20 steps, 0.0 ps. 77: 77: Writing final coordinates. 77: 77: Core t (s) Wall t (s) (%) 77: Time: 0.688 0.344 200.0 77: (ns/day) (hour/ns) 77: Performance: 5.273 4.551 77: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 77: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (360 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 77: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 77: ./src/programs/mdrun/tests/pmetest.cpp:331: Skipped 77: Test is being skipped because: 77: it targets GPU execution, but no compatible devices were detected 77: PME GPU does not support: 77: Non-GPU build of GROMACS. 77: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 77: [----------] 19 tests from ReproducesEnergies/PmeTest (151729 ms total) 77: 77: [----------] Global test environment tear-down 77: [==========] 19 tests from 1 test suite ran. (151765 ms total) 77: [ PASSED ] 4 tests. 77: [ SKIPPED ] 15 tests, listed below: 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 77: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 77/91 Test #77: MdrunMpi1RankPmeTests ........................ Passed 152.14 sec test 78 Start 78: MdrunMpi2RankPmeTests 78: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-mpi-pme-test" "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunMpi2RankPmeTests.xml" 78: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 78: Test timeout computed to be: 600 78: [==========] Running 19 tests from 1 test suite. 78: [----------] Global test environment set-up. 78: [----------] 19 tests from ReproducesEnergies/PmeTest 78: Setting the LD random seed to 1659600893 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: Number of degrees of freedom in T-Coupling group rest is 12.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 1046.791 K for 78: determining the Verlet buffer size 78: 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: This run will generate roughly 0 Mb of data 78: 78: There were 2 NOTEs 78: 78: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: For a correct single-point energy evaluation with nsteps = 0, use 78: continuation = yes to avoid constraining the input coordinates. 78: 78: Number of degrees of freedom in T-Coupling group rest is 13.00 78: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 78: 78: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: NVE simulation: will use the initial temperature of 966.268 K for 78: determining the Verlet buffer size 78: 78: 78: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_input.mdp]: 78: The optimal PME mesh load for parallel simulations is below 0.5 78: and for highly parallel simulations between 0.25 and 0.33, 78: for higher performance, increase the cut-off and the PME grid spacing. 78: 78: 78: 78: There were 3 NOTEs 78: Setting the LD random seed to -348405777 78: 78: Generated 8 of the 10 non-bonded parameter combinations 78: 78: Excluding 2 bonded neighbours molecule type 'Methanol' 78: 78: Excluding 2 bonded neighbours molecule type 'SOL' 78: 78: Searching the wall atom type(s) 78: 78: The largest distance between excluded atoms is 0.190 nm between atom 1 and 3 78: 78: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 78: 78: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 78: 78: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 78: 78: Note that mdrun will redetermine rlist based on the actual pair-list setup 78: Calculating fourier grid dimensions for X Y Z 78: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 78: 78: Estimate for the relative computational load of the PME mesh part: 1.00 78: 78: This run will generate roughly 0 Mb of data 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 23.9%. 78: The balanceable part of the MD step is 19%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 4.7%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: 78: NOTE: 11 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 14.922 3.731 400.0 78: (ns/day) (hour/ns) 78: Performance: 0.486 49.345 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_cpu (42168 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was turned on during the run due to measured imbalance. 78: Average load imbalance: 17.3%. 78: The balanceable part of the MD step is 22%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 3.8%. 78: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 78: 78: 78: NOTE: 12 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 13.107 3.277 400.0 78: (ns/day) (hour/ns) 78: Performance: 0.554 43.344 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_0_pme_auto.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_auto (3450 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 0 steps, 0.0 ps. 78: 78: NOTE: 18 % of the run time was spent in domain decomposition, 78: 2 % of the run time was spent in pair search, 78: you might want to increase nstlist (this has no effect on accuracy) 78: 78: NOTE: 5 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.390 0.098 399.6 78: (ns/day) (hour/ns) 78: Performance: 0.886 27.090 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_0_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_cpu (95604 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.544 0.386 399.8 78: (ns/day) (hour/ns) 78: Performance: 4.698 5.109 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_cpu (15011 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 1.472 0.368 399.8 78: (ns/day) (hour/ns) 78: Performance: 4.930 4.868 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_notunepme_npme_1_pme_auto.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_with_walls.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_auto (418 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 0 steps, 0.0 ps. 78: 78: Core t (s) Wall t (s) (%) 78: Time: 0.125 0.033 381.2 78: (ns/day) (hour/ns) 78: Performance: 2.632 9.117 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_with_walls_mdrun_notunepme_npme_1_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 [ OK ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_cpu (69818 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu (0 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu (8 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu 78: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_basic.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 78: Can not increase nstlist because an NVE ensemble is used 78: Using 2 MPI processes 78: Using 2 OpenMP threads per MPI process 78: 78: 78: NOTE: The number of threads is not equal to the number of (logical) cpus 78: and the -pin option is set to auto: will not pin threads to cpus. 78: This can lead to significant performance degradation. 78: Consider using -pin on (and -pinoffset in case you run multiple jobs). 78: starting mdrun 'spc-and-methanol' 78: 20 steps, 0.0 ps. 78: 78: Writing final coordinates. 78: 78: 78: Dynamic load balancing report: 78: DLB was off during the run due to low measured imbalance. 78: Average load imbalance: 10.2%. 78: The balanceable part of the MD step is 16%, load imbalance is computed from this. 78: Part of the total run time spent waiting due to load imbalance: 1.7%. 78: 78: 78: NOTE: 7 % of the run time was spent communicating energies, 78: you might want to increase some nst* mdp options 78: 78: Core t (s) Wall t (s) (%) 78: Time: 5.094 1.274 399.8 78: (ns/day) (hour/ns) 78: Performance: 1.424 16.853 78: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/ReproducesEnergies_PmeTest_Runs_basic_mdrun_tunepme_npme_0_pme_cpu.edr as single precision energy file 78: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_cpu (1403 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu (18 ms) 78: [ RUN ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu (0 ms) 78: [----------] 19 tests from ReproducesEnergies/PmeTest (227911 ms total) 78: 78: [----------] Global test environment tear-down 78: [==========] 19 tests from 1 test suite ran. (227963 ms total) 78: [ PASSED ] 7 tests. 78: [ SKIPPED ] 12 tests, listed below: 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_0_pme_gpu_pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_0_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_notunepme_npme_1_pme_gpu_pmefft_auto 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/with_walls_mdrun_notunepme_npme_1_pme_gpu_pmefft_gpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_cpu 78: [ SKIPPED ] ReproducesEnergies/PmeTest.Runs/basic_mdrun_tunepme_npme_0_pme_gpu_pmefft_gpu 78/91 Test #78: MdrunMpi2RankPmeTests ........................ Passed 228.27 sec test 79 Start 79: MdrunCoordinationBasicTests1Rank 79: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests1Rank.xml" 79: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 79: Test timeout computed to be: 1920 79: [==========] Running 1 test from 1 test suite. 79: [----------] Global test environment set-up. 79: [----------] 1 test from BasicPropagators/PeriodicActionsTest 79: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.002 0.002 97.8 79: (ns/day) (hour/ns) 79: Performance: 932.858 0.026 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (1) 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: There were 3 NOTEs 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.3 79: (ns/day) (hour/ns) 79: Performance: 2491.142 0.010 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: Setting nstcalcenergy (100) equal to nstenergy (4) 79: 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (1). 79: Other settings require a global communication frequency of 4. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 4. 79: 79: 79: There were 5 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.7 79: (ns/day) (hour/ns) 79: Performance: 2768.806 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (1). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.2 79: (ns/day) (hour/ns) 79: Performance: 2664.617 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (1). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 94.9 79: (ns/day) (hour/ns) 79: Performance: 2570.127 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: 79: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 79: that with the Verlet scheme, nstlist has no effect on the accuracy of 79: your simulation. 79: 79: 79: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 79: setting nstcomm equal to nstcalcenergy for less overhead 79: 79: Generated 1 of the 1 non-bonded parameter combinations 79: 79: Excluding 1 bonded neighbours molecule type 'Argon' 79: Number of degrees of freedom in T-Coupling group System is 33.00 79: 79: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: NVE simulation: will use the initial temperature of 68.810 K for 79: determining the Verlet buffer size 79: 79: 79: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 79: 79: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 79: 79: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 79: 79: Note that mdrun will redetermine rlist based on the actual pair-list setup 79: 79: This run will generate roughly 0 Mb of data 79: 79: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 79: COM removal frequency is set to (1). 79: Other settings require a global communication frequency of 100. 79: Note that this will require additional global communication steps, 79: which will reduce performance when using multiple ranks. 79: Consider setting nstcomm to a multiple of 100. 79: 79: 79: There were 4 NOTEs 79: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 79: Can not increase nstlist because an NVE ensemble is used 79: Using 1 MPI process 79: Using 1 OpenMP thread 79: 79: 79: NOTE: Thread affinity was not set. 79: starting mdrun 'Argon' 79: 16 steps, 0.0 ps. 79: 79: Writing final coordinates. 79: 79: Core t (s) Wall t (s) (%) 79: Time: 0.001 0.001 95.0 79: (ns/day) (hour/ns) 79: Performance: 2528.979 0.009 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 79: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 79: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (48 ms) 79: [----------] 1 test from BasicPropagators/PeriodicActionsTest (55 ms total) 79: 79: [----------] Global test environment tear-down 79: [==========] 1 test from 1 test suite ran. (63 ms total) 79: [ PASSED ] 1 test. 79/91 Test #79: MdrunCoordinationBasicTests1Rank ............. Passed 0.30 sec test 80 Start 80: MdrunCoordinationBasicTests2Ranks 80: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-basic-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationBasicTests2Ranks.xml" 80: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 80: Test timeout computed to be: 1920 80: [==========] Running 1 test from 1 test suite. 80: [----------] Global test environment set-up. 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest 80: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.8%. 80: The balanceable part of the MD step is 54%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.9%. 80: 80: 80: NOTE: 50 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.021 0.011 199.1 80: (ns/day) (hour/ns) 80: Performance: 137.283 0.175 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (1) 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: There were 3 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 1.6%. 80: The balanceable part of the MD step is 51%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 0.8%. 80: 80: 80: NOTE: 30 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.9 80: (ns/day) (hour/ns) 80: Performance: 1689.454 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: Setting nstcalcenergy (100) equal to nstenergy (4) 80: 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 4. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 4. 80: 80: 80: There were 5 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.6%. 80: The balanceable part of the MD step is 46%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 31 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.001 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1869.963 0.013 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 3.0%. 80: The balanceable part of the MD step is 45%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.3%. 80: 80: 80: NOTE: 35 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.5 80: (ns/day) (hour/ns) 80: Performance: 1693.634 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.3%. 80: The balanceable part of the MD step is 48%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.1%. 80: 80: 80: NOTE: 33 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 189.1 80: (ns/day) (hour/ns) 80: Performance: 1679.551 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: 80: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 80: that with the Verlet scheme, nstlist has no effect on the accuracy of 80: your simulation. 80: 80: 80: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 80: setting nstcomm equal to nstcalcenergy for less overhead 80: 80: Number of degrees of freedom in T-Coupling group System is 33.00 80: 80: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: NVE simulation: will use the initial temperature of 68.810 K for 80: determining the Verlet buffer size 80: 80: 80: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 80: COM removal frequency is set to (1). 80: Other settings require a global communication frequency of 100. 80: Note that this will require additional global communication steps, 80: which will reduce performance when using multiple ranks. 80: Consider setting nstcomm to a multiple of 100. 80: 80: 80: There were 4 NOTEs 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Generated 1 of the 1 non-bonded parameter combinations 80: 80: Excluding 1 bonded neighbours molecule type 'Argon' 80: 80: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 80: 80: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 80: 80: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 80: 80: Note that mdrun will redetermine rlist based on the actual pair-list setup 80: 80: This run will generate roughly 0 Mb of data 80: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 80: Can not increase nstlist because an NVE ensemble is used 80: Using 2 MPI processes 80: Using 1 OpenMP thread per MPI process 80: 80: 80: NOTE: The number of threads is not equal to the number of (logical) cpus 80: and the -pin option is set to auto: will not pin threads to cpus. 80: This can lead to significant performance degradation. 80: Consider using -pin on (and -pinoffset in case you run multiple jobs). 80: starting mdrun 'Argon' 80: 16 steps, 0.0 ps. 80: 80: Writing final coordinates. 80: 80: 80: Dynamic load balancing report: 80: DLB was off during the run due to low measured imbalance. 80: Average load imbalance: 2.6%. 80: The balanceable part of the MD step is 45%, load imbalance is computed from this. 80: Part of the total run time spent waiting due to load imbalance: 1.2%. 80: 80: 80: NOTE: 34 % of the run time was spent communicating energies, 80: you might want to increase some nst* mdp options 80: 80: Core t (s) Wall t (s) (%) 80: Time: 0.002 0.001 188.9 80: (ns/day) (hour/ns) 80: Performance: 1769.523 0.014 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 80: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 80: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (166 ms) 80: [----------] 1 test from BasicPropagators/PeriodicActionsTest (170 ms total) 80: 80: [----------] Global test environment tear-down 80: [==========] 1 test from 1 test suite ran. (182 ms total) 80: [ PASSED ] 1 test. 80/91 Test #80: MdrunCoordinationBasicTests2Ranks ............ Passed 0.56 sec test 81 Start 81: MdrunCoordinationCouplingTests1Rank 81: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests1Rank.xml" 81: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 81: Test timeout computed to be: 1920 81: [==========] Running 25 tests from 1 test suite. 81: [----------] Global test environment set-up. 81: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.006 0.006 98.8 81: (ns/day) (hour/ns) 81: Performance: 254.244 0.094 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 2163.130 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.009 0.009 99.6 81: (ns/day) (hour/ns) 81: Performance: 164.713 0.146 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 2216.838 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2543.598 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2572.273 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (108 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1947.090 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.1 81: (ns/day) (hour/ns) 81: Performance: 2345.999 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2546.752 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2319.501 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2517.611 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2589.573 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (114 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.8 81: (ns/day) (hour/ns) 81: Performance: 1941.568 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 2383.208 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.4 81: (ns/day) (hour/ns) 81: Performance: 2658.867 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2396.186 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.1 81: (ns/day) (hour/ns) 81: Performance: 2517.611 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.3 81: (ns/day) (hour/ns) 81: Performance: 2451.490 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (182 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 1958.853 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2283.393 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.1 81: (ns/day) (hour/ns) 81: Performance: 2648.579 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.5 81: (ns/day) (hour/ns) 81: Performance: 2545.700 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.8 81: (ns/day) (hour/ns) 81: Performance: 2443.710 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 2480.110 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (170 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 2128.012 0.011 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 2413.080 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.000 0.001 94.5 81: (ns/day) (hour/ns) 81: Performance: 2858.744 0.008 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.8 81: (ns/day) (hour/ns) 81: Performance: 2608.211 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 2576.576 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.8 81: (ns/day) (hour/ns) 81: Performance: 2565.845 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (152 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1936.685 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2361.285 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.3 81: (ns/day) (hour/ns) 81: Performance: 2622.645 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.0 81: (ns/day) (hour/ns) 81: Performance: 2420.666 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.3 81: (ns/day) (hour/ns) 81: Performance: 2553.085 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (150 ms) 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2361.285 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 1906.124 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.018 0.018 99.7 81: (ns/day) (hour/ns) 81: Performance: 80.815 0.297 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 90.1 81: (ns/day) (hour/ns) 81: Performance: 2438.873 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2396.186 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 2342.431 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.4 81: (ns/day) (hour/ns) 81: Performance: 2354.067 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (143 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 1978.989 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2226.452 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.5 81: (ns/day) (hour/ns) 81: Performance: 2488.123 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.5 81: (ns/day) (hour/ns) 81: Performance: 2350.475 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.7 81: (ns/day) (hour/ns) 81: Performance: 2381.366 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.7 81: (ns/day) (hour/ns) 81: Performance: 2326.508 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (78 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.8 81: (ns/day) (hour/ns) 81: Performance: 2054.216 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2481.109 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.7 81: (ns/day) (hour/ns) 81: Performance: 2654.284 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2492.150 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2484.110 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.9 81: (ns/day) (hour/ns) 81: Performance: 2465.224 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (107 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 1996.304 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.9 81: (ns/day) (hour/ns) 81: Performance: 2312.535 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: or new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: and should not be used fGenerated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.4 81: (ns/day) (hour/ns) 81: Performance: 2562.643 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 2495.178 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.3 81: (ns/day) (hour/ns) 81: Performance: 2406.482 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.0 81: (ns/day) (hour/ns) 81: Performance: 2405.542 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (109 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 1910.262 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2245.933 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.3 81: (ns/day) (hour/ns) 81: Performance: 2487.119 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 2413.080 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 2373.110 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 2388.753 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (135 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 2002.143 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.9 81: (ns/day) (hour/ns) 81: Performance: 2285.935 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.5 81: (ns/day) (hour/ns) 81: Performance: 2621.529 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.5 81: (ns/day) (hour/ns) 81: Performance: 2447.594 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.7 81: (ns/day) (hour/ns) 81: Performance: 2399.920 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 81: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 81: 1 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 2460.301 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (210 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.5 81: (ns/day) (hour/ns) 81: Performance: 2004.749 0.012 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.017 0.017 99.7 81: (ns/day) (hour/ns) 81: Performance: 86.818 0.276 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2434.055 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 3 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 2478.115 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 2299.587 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 3 NOTEs 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.014 0.014 99.8 81: (ns/day) (hour/ns) 81: Performance: 103.061 0.233 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (103 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1903.180 0.013 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.005 0.005 99.2 81: (ns/day) (hour/ns) 81: Performance: 301.724 0.080 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2542.548 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2266.591 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.8 81: (ns/day) (hour/ns) 81: Performance: 2284.239 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2345.999 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (85 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 1821.583 0.013 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 2183.833 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.9 81: (ns/day) (hour/ns) 81: Performance: 2327.387 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2230.483 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2310.800 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.7 81: (ns/day) (hour/ns) 81: Performance: 2327.387 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (147 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.2 81: (ns/day) (hour/ns) 81: Performance: 1939.734 0.012 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 2196.290 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 2571.199 0.009 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2209.682 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.4 81: (ns/day) (hour/ns) 81: Performance: 2368.548 0.010 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 2257.455 0.011 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (99 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.5 81: (ns/day) (hour/ns) 81: Performance: 1576.002 0.015 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.7 81: (ns/day) (hour/ns) 81: Performance: 1780.518 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 4. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 4. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.6 81: (ns/day) (hour/ns) 81: Performance: 1933.645 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.7 81: (ns/day) (hour/ns) 81: Performance: 1745.705 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1751.662 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 100. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 100. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1741.757 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (68 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.1 81: (ns/day) (hour/ns) 81: Performance: 1543.235 0.016 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.8 81: (ns/day) (hour/ns) 81: Performance: 1642.825 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.6 81: (ns/day) (hour/ns) 81: Performance: 1845.594 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.7 81: (ns/day) (hour/ns) 81: Performance: 1768.761 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.9 81: (ns/day) (hour/ns) 81: Performance: 1792.955 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1693.401 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (60 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.009 0.009 99.6 81: (ns/day) (hour/ns) 81: Performance: 159.684 0.150 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.8 81: (ns/day) (hour/ns) 81: Performance: 1598.908 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.9 81: (ns/day) (hour/ns) 81: Performance: 1829.155 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.9 81: (ns/day) (hour/ns) 81: Performance: 1774.876 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.0 81: (ns/day) (hour/ns) 81: Performance: 1683.222 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 81: NVE simulation: will use the initial temperature of 68.810 K for 81: determining the Verlet buffer size 81: 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Can not increase nstlist because an NVE ensemble is used 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.7 81: (ns/day) (hour/ns) 81: Performance: 1735.867 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (66 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1564.794 0.015 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.3 81: (ns/day) (hour/ns) 81: Performance: 1738.317 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 2032.528 0.012 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1894.984 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1866.847 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1145.731 0.021 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (48 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1508.101 0.016 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 1697.133 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1365.380 0.018 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.8 81: (ns/day) (hour/ns) 81: Performance: 1660.537 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.5 81: (ns/day) (hour/ns) 81: Performance: 1705.119 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 81: The Berendsen barostat does not generate any strictly correct ensemble, 81: and should not be used for new production simulations (in our opinion). 81: We recommend using the C-rescale barostat instead. 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: 81: There was 1 WARNING 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1692.006 0.014 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (31 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.0 81: (ns/day) (hour/ns) 81: Performance: 1422.441 0.017 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.2 81: (ns/day) (hour/ns) 81: Performance: 1223.797 0.020 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1829.155 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.7 81: (ns/day) (hour/ns) 81: Performance: 1787.752 0.013 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.6 81: (ns/day) (hour/ns) 81: Performance: 1734.890 0.014 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.2 81: (ns/day) (hour/ns) 81: Performance: 1646.777 0.015 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (32 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 97.1 81: (ns/day) (hour/ns) 81: Performance: 1354.572 0.018 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 2 NOTEs 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.6 81: (ns/day) (hour/ns) 81: Performance: 1460.202 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: Reading file /build/reproducible-path/gromacs-2024.4/Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.5 81: (ns/day) (hour/ns) 81: Performance: 1488.426 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.2 81: (ns/day) (hour/ns) 81: Performance: 1501.119 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.3 81: (ns/day) (hour/ns) 81: Performance: 1475.238 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.7 81: (ns/day) (hour/ns) 81: Performance: 1428.709 0.017 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (35 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 95.0 81: (ns/day) (hour/ns) 81: Performance: 1027.108 0.023 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: There were 3 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.3 81: (ns/day) (hour/ns) 81: Performance: 1103.456 0.022 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.3 81: (ns/day) (hour/ns) 81: Performance: 1196.000 0.020 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.4 81: (ns/day) (hour/ns) 81: Performance: 1152.806 0.021 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.2 81: (ns/day) (hour/ns) 81: Performance: 1161.281 0.021 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: 81: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: for current Trotter decomposition methods with vv, nsttcouple and 81: nstpcouple must be equal. Both have been reset to 81: min(nsttcouple,nstpcouple) = 2 81: 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 81: COM removal frequency is set to (5). 81: Other settings require a global communication frequency of 2. 81: Note that this will require additional global communication steps, 81: which will reduce performance when using multiple ranks. 81: Consider setting nstcomm to a multiple of 2. 81: 81: 81: There were 4 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.4 81: (ns/day) (hour/ns) 81: Performance: 1049.505 0.023 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (36 ms) 81: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.8 81: (ns/day) (hour/ns) 81: Performance: 1265.269 0.019 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (1) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.4 81: (ns/day) (hour/ns) 81: Performance: 1288.288 0.019 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: Setting nstcalcenergy (100) equal to nstenergy (4) 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 94.6 81: (ns/day) (hour/ns) 81: Performance: 1428.047 0.017 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 1457.094 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.6 81: (ns/day) (hour/ns) 81: Performance: 1429.372 0.017 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: 81: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 81: that with the Verlet scheme, nstlist has no effect on the accuracy of 81: your simulation. 81: 81: 81: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 81: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 81: setting nstcomm equal to nstcalcenergy for less overhead 81: 81: Generated 1 of the 1 non-bonded parameter combinations 81: 81: Excluding 1 bonded neighbours molecule type 'Argon' 81: Number of degrees of freedom in T-Coupling group System is 33.00 81: 81: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 81: 81: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 81: 81: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 81: 81: Note that mdrun will redetermine rlist based on the actual pair-list setup 81: 81: This run will generate roughly 0 Mb of data 81: 81: There were 2 NOTEs 81: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 81: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 81: 81: Using 1 MPI process 81: Using 1 OpenMP thread 81: 81: 81: NOTE: Thread affinity was not set. 81: starting mdrun 'Argon' 81: 16 steps, 0.0 ps. 81: 81: Writing final coordinates. 81: 81: Core t (s) Wall t (s) (%) 81: Time: 0.001 0.001 96.1 81: (ns/day) (hour/ns) 81: Performance: 1473.121 0.016 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 81: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 81: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (43 ms) 81: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (2647 ms total) 81: 81: [----------] Global test environment tear-down 81: [==========] 25 tests from 1 test suite ran. (2651 ms total) 81: [ PASSED ] 25 tests. 81/91 Test #81: MdrunCoordinationCouplingTests1Rank .......... Passed 3.12 sec test 82 Start 82: MdrunCoordinationCouplingTests2Ranks 82: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-coupling-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationCouplingTests2Ranks.xml" 82: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 82: Test timeout computed to be: 1920 82: [==========] Running 25 tests from 1 test suite. 82: [----------] Global test environment set-up. 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 92 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.031 0.041 74.8 82: (ns/day) (hour/ns) 82: Performance: 35.618 0.674 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.1 82: (ns/day) (hour/ns) 82: Performance: 1673.392 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.1%. 82: The balanceable part of the MD step is 40%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.0 82: (ns/day) (hour/ns) 82: Performance: 1998.895 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 4.1%. 82: The balanceable part of the MD step is 35%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.4%. 82: 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.7 82: (ns/day) (hour/ns) 82: Performance: 1852.532 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 4.4%. 82: The balanceable part of the MD step is 38%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.6%. 82: 82: 82: NOTE: 33 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.6 82: (ns/day) (hour/ns) 82: Performance: 1798.976 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.0%. 82: The balanceable part of the MD step is 37%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.3 82: (ns/day) (hour/ns) 82: Performance: 1919.487 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (661 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.7%. 82: The balanceable part of the MD step is 53%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.1 82: (ns/day) (hour/ns) 82: Performance: 1495.653 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.5 82: (ns/day) (hour/ns) 82: Performance: 1627.419 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 47%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 1944.632 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.8 82: (ns/day) (hour/ns) 82: Performance: 1801.343 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.4%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.8 82: (ns/day) (hour/ns) 82: Performance: 1786.197 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.7%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 1802.925 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (431 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.7%. 82: The balanceable part of the MD step is 55%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 28 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.9 82: (ns/day) (hour/ns) 82: Performance: 1481.981 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.5%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.3%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.0 82: (ns/day) (hour/ns) 82: Performance: 1643.702 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.8 82: (ns/day) (hour/ns) 82: Performance: 1831.058 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 22.9%. 82: The balanceable part of the MD step is 20%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 4.5%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 26 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 43 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.172 0.086 199.9 82: (ns/day) (hour/ns) 82: Performance: 17.043 1.408 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.6%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.6 82: (ns/day) (hour/ns) 82: Performance: 1816.748 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.2%. 82: The balanceable part of the MD step is 39%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.5%. 82: 82: 82: NOTE: 11 % of the run time was spent in domain decomposition, 82: 3 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 1684.603 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1000 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 53%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.8 82: (ns/day) (hour/ns) 82: Performance: 1455.029 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.2%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.9 82: (ns/day) (hour/ns) 82: Performance: 1643.263 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.9%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.6 82: (ns/day) (hour/ns) 82: Performance: 1860.644 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 1810.342 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.0%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.1 82: (ns/day) (hour/ns) 82: Performance: 1755.405 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1781.291 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (493 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.3 82: (ns/day) (hour/ns) 82: Performance: 1635.845 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.5 82: (ns/day) (hour/ns) 82: Performance: 1816.213 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.3 82: (ns/day) (hour/ns) 82: Performance: 1961.348 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.1 82: (ns/day) (hour/ns) 82: Performance: 2077.772 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.1 82: (ns/day) (hour/ns) 82: Performance: 2054.901 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 97 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.042 0.021 199.4 82: (ns/day) (hour/ns) 82: Performance: 69.974 0.343 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (498 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.023 7.7 82: (ns/day) (hour/ns) 82: Performance: 63.697 0.377 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.9 82: (ns/day) (hour/ns) 82: Performance: 1740.035 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.1 82: (ns/day) (hour/ns) 82: Performance: 1976.767 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.1 82: (ns/day) (hour/ns) 82: Performance: 1949.863 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.1 82: (ns/day) (hour/ns) 82: Performance: 1958.542 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.2 82: (ns/day) (hour/ns) 82: Performance: 1882.247 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (479 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.9 82: (ns/day) (hour/ns) 82: Performance: 1597.043 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 58 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.146 0.073 199.8 82: (ns/day) (hour/ns) 82: Performance: 20.105 1.194 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.4 82: (ns/day) (hour/ns) 82: Performance: 1887.437 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.1 82: (ns/day) (hour/ns) 82: Performance: 1895.859 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.2 82: (ns/day) (hour/ns) 82: Performance: 1959.165 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 186.9 82: (ns/day) (hour/ns) 82: Performance: 1915.012 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (830 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.3 82: (ns/day) (hour/ns) 82: Performance: 1486.989 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 1736.601 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 33 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.8 82: (ns/day) (hour/ns) 82: Performance: 2022.187 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.5 82: (ns/day) (hour/ns) 82: Performance: 1869.679 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.7 82: (ns/day) (hour/ns) 82: Performance: 1889.173 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.4 82: (ns/day) (hour/ns) 82: Performance: 1835.969 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (276 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.8 82: (ns/day) (hour/ns) 82: Performance: 1531.153 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 33 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.2 82: (ns/day) (hour/ns) 82: Performance: 1635.194 0.015 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.4 82: (ns/day) (hour/ns) 82: Performance: 1999.544 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 41 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.269 0.134 199.9 82: (ns/day) (hour/ns) 82: Performance: 10.929 2.196 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.6 82: (ns/day) (hour/ns) 82: Performance: 1873.945 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.2 82: (ns/day) (hour/ns) 82: Performance: 1928.500 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (570 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.3 82: (ns/day) (hour/ns) 82: Performance: 1511.988 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1741.511 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 186.3 82: (ns/day) (hour/ns) 82: Performance: 1890.043 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.3 82: (ns/day) (hour/ns) 82: Performance: 1780.261 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.0 82: (ns/day) (hour/ns) 82: Performance: 1954.813 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.5 82: (ns/day) (hour/ns) 82: Performance: 1874.230 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (837 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.8 82: (ns/day) (hour/ns) 82: Performance: 1483.229 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: There were 3 NOTEs 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.7 82: (ns/day) (hour/ns) 82: Performance: 1662.105 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 33 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 186.4 82: (ns/day) (hour/ns) 82: Performance: 2001.818 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.3 82: (ns/day) (hour/ns) 82: Performance: 1938.513 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.6 82: (ns/day) (hour/ns) 82: Performance: 2000.842 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.0 82: (ns/day) (hour/ns) 82: Performance: 1955.744 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1173 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 29 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.2 82: (ns/day) (hour/ns) 82: Performance: 1573.185 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.9 82: (ns/day) (hour/ns) 82: Performance: 1867.696 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.5 82: (ns/day) (hour/ns) 82: Performance: 1933.949 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 186.9 82: (ns/day) (hour/ns) 82: Performance: 1969.185 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 3 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.8 82: (ns/day) (hour/ns) 82: Performance: 1978.036 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 82: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 82: 1 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 186.7 82: (ns/day) (hour/ns) 82: Performance: 1901.418 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (429 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 191.1 82: (ns/day) (hour/ns) 82: Performance: 1557.082 0.015 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.8 82: (ns/day) (hour/ns) 82: Performance: 1777.693 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 3 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.3 82: (ns/day) (hour/ns) 82: Performance: 2103.310 0.011 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.7 82: (ns/day) (hour/ns) 82: Performance: 2031.523 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 187.2 82: (ns/day) (hour/ns) 82: Performance: 2032.864 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.0 82: (ns/day) (hour/ns) 82: Performance: 1907.895 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (999 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.3 82: (ns/day) (hour/ns) 82: Performance: 1508.101 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 32 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.2 82: (ns/day) (hour/ns) 82: Performance: 1724.449 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 34 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1948.938 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 11 % of the run time was spent in domain decomposition, 82: 0 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 44 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.490 0.245 200.0 82: (ns/day) (hour/ns) 82: Performance: 6.000 4.000 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.2 82: (ns/day) (hour/ns) 82: Performance: 1924.584 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.6 82: (ns/day) (hour/ns) 82: Performance: 1897.903 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1318 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 190.4 82: (ns/day) (hour/ns) 82: Performance: 1533.058 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.4 82: (ns/day) (hour/ns) 82: Performance: 1738.071 0.014 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 33 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 2115.225 0.011 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 36 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.4 82: (ns/day) (hour/ns) 82: Performance: 1934.556 0.012 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 189.4 82: (ns/day) (hour/ns) 82: Performance: 1864.304 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: 82: NOTE: 51 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 1.820 0.944 192.8 82: (ns/day) (hour/ns) 82: Performance: 1.556 15.423 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (2080 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 30 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 189.9 82: (ns/day) (hour/ns) 82: Performance: 1528.494 0.016 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 31 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.017 9.7 82: (ns/day) (hour/ns) 82: Performance: 86.610 0.277 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 35 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 189.0 82: (ns/day) (hour/ns) 82: Performance: 1908.191 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.6 82: (ns/day) (hour/ns) 82: Performance: 1826.173 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.001 0.001 188.5 82: (ns/day) (hour/ns) 82: Performance: 1881.959 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 37 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 188.2 82: (ns/day) (hour/ns) 82: Performance: 1803.981 0.013 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (348 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.4%. 82: The balanceable part of the MD step is 54%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.036 0.018 199.0 82: (ns/day) (hour/ns) 82: Performance: 81.300 0.295 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.1%. 82: The balanceable part of the MD step is 59%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.3%. 82: 82: 82: NOTE: 28 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 187.2 82: (ns/day) (hour/ns) 82: Performance: 1120.821 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 4. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 4. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.2%. 82: The balanceable part of the MD step is 48%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.6%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 186.7 82: (ns/day) (hour/ns) 82: Performance: 1297.923 0.018 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.3%. 82: The balanceable part of the MD step is 44%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 185.6 82: (ns/day) (hour/ns) 82: Performance: 1278.397 0.019 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 45%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.8%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 185.3 82: (ns/day) (hour/ns) 82: Performance: 1302.176 0.018 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (275 ms) 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 100. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 100. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.1%. 82: The balanceable part of the MD step is 46%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.0%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.5 82: (ns/day) (hour/ns) 82: Performance: 1273.639 0.019 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 0.6%. 82: The balanceable part of the MD step is 59%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.3%. 82: 82: 82: NOTE: 24 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 187.5 82: (ns/day) (hour/ns) 82: Performance: 1032.531 0.023 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 59%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: NOTE: 27 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 186.6 82: (ns/day) (hour/ns) 82: Performance: 1132.254 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 12.8%. 82: The balanceable part of the MD step is 34%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 4.3%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: 82: NOTE: 62 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.119 0.060 199.7 82: (ns/day) (hour/ns) 82: Performance: 24.648 0.974 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 28 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 185.9 82: (ns/day) (hour/ns) 82: Performance: 1144.029 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 12.3%. 82: The balanceable part of the MD step is 3%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.4%. 82: 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.021 0.010 198.0 82: (ns/day) (hour/ns) 82: Performance: 140.058 0.171 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.8%. 82: The balanceable part of the MD step is 51%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 0 % of the run time was spent in domain decomposition, 82: 18 % of the run time was spent in pair search, 82: you might want to increase nstlist (this has no effect on accuracy) 82: 82: NOTE: 79 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.071 0.046 152.4 82: (ns/day) (hour/ns) 82: Performance: 31.655 0.758 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (265 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.5%. 82: The balanceable part of the MD step is 60%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.9%. 82: 82: 82: NOTE: 25 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 187.6 82: (ns/day) (hour/ns) 82: Performance: 995.812 0.024 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was turned on during the run due to measured imbalance. 82: Average load imbalance: 91.1%. 82: The balanceable part of the MD step is 12%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 10.6%. 82: Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % 82: 82: NOTE: 10.6 % of the available CPU time was lost due to load imbalance 82: in the domain decomposition. 82: You can consider manually changing the decomposition (option -dd); 82: e.g. by using fewer domains along the box dimension in which there is 82: considerable inhomogeneity in the simulated system. 82: 82: NOTE: 66 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.068 0.034 199.4 82: (ns/day) (hour/ns) 82: Performance: 42.890 0.560 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 1.3%. 82: The balanceable part of the MD step is 57%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 0.7%. 82: 82: 82: NOTE: 27 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 186.5 82: (ns/day) (hour/ns) 82: Performance: 1125.428 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.0%. 82: The balanceable part of the MD step is 52%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.1%. 82: 82: 82: NOTE: 28 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 186.2 82: (ns/day) (hour/ns) 82: Performance: 1077.215 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 3.4%. 82: The balanceable part of the MD step is 48%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.6%. 82: 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.014 198.4 82: (ns/day) (hour/ns) 82: Performance: 108.194 0.222 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_input.mdp]: 82: NVE simulation: will use the initial temperature of 68.810 K for 82: determining the Verlet buffer size 82: 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Can not increase nstlist because an NVE ensemble is used 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: 82: Dynamic load balancing report: 82: DLB was off during the run due to low measured imbalance. 82: Average load imbalance: 2.6%. 82: The balanceable part of the MD step is 50%, load imbalance is computed from this. 82: Part of the total run time spent waiting due to load imbalance: 1.3%. 82: 82: 82: NOTE: 48 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.027 0.014 198.2 82: (ns/day) (hour/ns) 82: Performance: 107.923 0.222 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_18.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/18 (190 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 61 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.107 0.054 199.6 82: (ns/day) (hour/ns) 82: Performance: 27.386 0.876 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 6 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.004 0.002 190.6 82: (ns/day) (hour/ns) 82: Performance: 726.828 0.033 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.2 82: (ns/day) (hour/ns) 82: Performance: 1342.031 0.018 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 71 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.122 0.061 199.4 82: (ns/day) (hour/ns) 82: Performance: 24.080 0.997 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 7 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.1 82: (ns/day) (hour/ns) 82: Performance: 1167.332 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 7 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.9 82: (ns/day) (hour/ns) 82: Performance: 1211.523 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_19.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/19 (396 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 185.3 82: (ns/day) (hour/ns) 82: Performance: 1016.851 0.024 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 184.5 82: (ns/day) (hour/ns) 82: Performance: 1055.438 0.023 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_inputOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 .mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.9 82: (ns/day) (hour/ns) 82: Performance: 1192.989 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.8 82: (ns/day) (hour/ns) 82: Performance: 1118.583 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.9 82: (ns/day) (hour/ns) 82: Performance: 1131.422 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: 82: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_input.mdp]: 82: The Berendsen barostat does not generate any strictly correct ensemble, 82: and should not be used for new production simulations (in our opinion). 82: We recommend using the C-rescale barostat instead. 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: 82: There was 1 WARNING 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.5 82: (ns/day) (hour/ns) 82: Performance: 1139.795 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_20.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/20 (443 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 184.9 82: (ns/day) (hour/ns) 82: Performance: 1013.506 0.024 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 185.0 82: (ns/day) (hour/ns) 82: Performance: 1090.178 0.022 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.7 82: (ns/day) (hour/ns) 82: Performance: 1192.642 0.020 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 183.9 82: (ns/day) (hour/ns) 82: Performance: 1137.165 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.035 0.018 198.1 82: (ns/day) (hour/ns) 82: Performance: 82.649 0.290 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 9 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.002 0.001 184.1 82: (ns/day) (hour/ns) 82: Performance: 1129.555 0.021 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_21.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/21 (526 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 187.4 82: (ns/day) (hour/ns) 82: Performance: 923.489 0.026 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: Writing final coordinates. 82: 82: NOTE: 59 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.136 0.069 195.7 82: (ns/day) (hour/ns) 82: Performance: 21.159 1.134 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 6 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.004 0.002 190.9 82: (ns/day) (hour/ns) 82: Performance: 734.059 0.033 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 186.4 82: (ns/day) (hour/ns) 82: Performance: 1045.143 0.023 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 186.7 82: (ns/day) (hour/ns) 82: Performance: 965.081 0.025 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupliOpened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: ng_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.032 0.016 198.0 82: (ns/day) (hour/ns) 82: Performance: 89.856 0.267 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_22.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/22 (387 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 64 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.100 0.064 155.5 82: (ns/day) (hour/ns) 82: Performance: 22.916 1.047 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 3 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 7 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 187.4 82: (ns/day) (hour/ns) 82: Performance: 833.414 0.029 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 7 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 186.5 82: (ns/day) (hour/ns) 82: Performance: 879.645 0.027 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 7 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 187.2 82: (ns/day) (hour/ns) 82: Performance: 816.027 0.029 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 7 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 186.1 82: (ns/day) (hour/ns) 82: Performance: 802.317 0.030 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: for current Trotter decomposition methods with vv, nsttcouple and 82: nstpcouple must be equal. Both have been reset to 82: min(nsttcouple,nstpcouple) = 2 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_input.mdp]: 82: COM removal frequency is set to (5). 82: Other settings require a global communication frequency of 2. 82: Note that this will require additional global communication steps, 82: which will reduce performance when using multiple ranks. 82: Consider setting nstcomm to a multiple of 2. 82: 82: 82: There were 4 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 7 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 187.0 82: (ns/day) (hour/ns) 82: Performance: 815.973 0.029 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_23.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/23 (407 ms) 82: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 186.9 82: (ns/day) (hour/ns) 82: Performance: 871.618 0.028 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (1) 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.066 0.033 199.3 82: (ns/day) (hour/ns) 82: Performance: 44.413 0.540 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: Setting nstcalcenergy (100) equal to nstenergy (4) 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 81 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.188 0.094 199.8 82: (ns/day) (hour/ns) 82: Performance: 15.581 1.540 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: 82: There were 2 NOTEs 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.001 185.3 82: (ns/day) (hour/ns) 82: Performance: 1003.272 0.024 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 186.0 82: (ns/day) (hour/ns) 82: Performance: 962.518 0.025 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: 82: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 82: that with the Verlet scheme, nstlist has no effect on the accuracy of 82: your simulation. 82: 82: 82: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_input.mdp]: 82: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 82: setting nstcomm equal to nstcalcenergy for less overhead 82: 82: Number of degrees of freedom in T-Coupling group System is 33.00 82: 82: There were 2 NOTEs 82: Generated 1 of the 1 non-bonded parameter combinations 82: 82: Excluding 1 bonded neighbours molecule type 'Argon' 82: 82: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 82: 82: Calculated rlist for 1x1 atom pair-list as 0.703 nm, buffer size 0.003 nm 82: 82: Set rlist, assuming 4x4 atom pair-list, to 0.703 nm, buffer size 0.003 nm 82: 82: Note that mdrun will redetermine rlist based on the actual pair-list setup 82: 82: This run will generate roughly 0 Mb of data 82: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 82: Changing nstlist from 8 to 100, rlist from 0.703 to 0.751 82: 82: Using 2 MPI processes 82: Using 1 OpenMP thread per MPI process 82: 82: 82: NOTE: The number of threads is not equal to the number of (logical) cpus 82: and the -pin option is set to auto: will not pin threads to cpus. 82: This can lead to significant performance degradation. 82: Consider using -pin on (and -pinoffset in case you run multiple jobs). 82: starting mdrun 'Argon' 82: 16 steps, 0.0 ps. 82: 82: Writing final coordinates. 82: 82: NOTE: 8 % of the run time was spent communicating energies, 82: you might want to increase some nst* mdp options 82: 82: Core t (s) Wall t (s) (%) 82: Time: 0.003 0.002 185.1 82: (ns/day) (hour/ns) 82: Performance: 962.818 0.025 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24_reference.edr as single precision energy file 82: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_24.edr as single precision energy file 82: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/24 (1363 ms) 82: [----------] 25 tests from PropagatorsWithCoupling/PeriodicActionsTest (16899 ms total) 82: 82: [----------] Global test environment tear-down 82: [==========] 25 tests from 1 test suite ran. (16910 ms total) 82: [ PASSED ] 25 tests. 82/91 Test #82: MdrunCoordinationCouplingTests2Ranks ......... Passed 17.38 sec test 83 Start 83: MdrunCoordinationConstraintsTests1Rank 83: Test command: /usr/bin/mpiexec "-n" "1" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests1Rank.xml" 83: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 83: Test timeout computed to be: 1920 83: [==========] Running 13 tests from 1 test suite. 83: [----------] Global test environment set-up. 83: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.5 83: (ns/day) (hour/ns) 83: Performance: 1603.486 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.017 99.7 83: (ns/day) (hour/ns) 83: Performance: 86.532 0.277 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 93.7 83: (ns/day) (hour/ns) 83: Performance: 2237.775 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.0 83: (ns/day) (hour/ns) 83: Performance: 2156.316 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.037 0.037 99.9 83: (ns/day) (hour/ns) 83: Performance: 39.808 0.603 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: NOTE: 96 % of the run time was spent in pair search, 83: you might want to increase nstlist (this has no effect on accuracy) 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.021 0.021 99.8 83: (ns/day) (hour/ns) 83: Performance: 70.165 0.342 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (4887 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.2 83: (ns/day) (hour/ns) 83: Performance: 1472.769 0.016 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.5 83: (ns/day) (hour/ns) 83: Performance: 2004.749 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 93.4 83: (ns/day) (hour/ns) 83: Performance: 2222.436 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 93.6 83: (ns/day) (hour/ns) 83: Performance: 2140.582 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.4 83: (ns/day) (hour/ns) 83: Performance: 1912.040 0.013 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.4 83: (ns/day) (hour/ns) 83: Performance: 2128.012 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (4780 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.013 0.013 99.6 83: (ns/day) (hour/ns) 83: Performance: 111.599 0.215 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.2 83: (ns/day) (hour/ns) 83: Performance: 1876.513 0.013 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 93.8 83: (ns/day) (hour/ns) 83: Performance: 2346.893 0.010 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.2 83: (ns/day) (hour/ns) 83: Performance: 2183.833 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 93.3 83: (ns/day) (hour/ns) 83: Performance: 2246.752 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.3 83: (ns/day) (hour/ns) 83: Performance: 1885.704 0.013 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (4400 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.8 83: (ns/day) (hour/ns) 83: Performance: 1841.182 0.013 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.037 0.037 99.8 83: (ns/day) (hour/ns) 83: Performance: 39.753 0.604 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.2 83: (ns/day) (hour/ns) 83: Performance: 2173.049 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.2 83: (ns/day) (hour/ns) 83: Performance: 2285.087 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.4 83: (ns/day) (hour/ns) 83: Performance: 2349.578 0.010 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.033 0.033 99.8 83: (ns/day) (hour/ns) 83: Performance: 44.593 0.538 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (4939 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.6 83: (ns/day) (hour/ns) 83: Performance: 1660.090 0.014 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.009 0.009 99.4 83: (ns/day) (hour/ns) 83: Performance: 158.713 0.151 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.6 83: (ns/day) (hour/ns) 83: Performance: 2230.483 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.7 83: (ns/day) (hour/ns) 83: Performance: 2123.610 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.6 83: (ns/day) (hour/ns) 83: Performance: 2101.874 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.6 83: (ns/day) (hour/ns) 83: Performance: 2070.788 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4602 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.8 83: (ns/day) (hour/ns) 83: Performance: 1739.789 0.014 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.8 83: (ns/day) (hour/ns) 83: Performance: 2006.708 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.7 83: (ns/day) (hour/ns) 83: Performance: 2380.446 0.010 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.2 83: (ns/day) (hour/ns) 83: Performance: 2205.726 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.5 83: (ns/day) (hour/ns) 83: Performance: 2203.360 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.1 83: (ns/day) (hour/ns) 83: Performance: 2122.879 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2087 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.2 83: (ns/day) (hour/ns) 83: Performance: 1657.856 0.014 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.2 83: (ns/day) (hour/ns) 83: Performance: 1941.568 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.8 83: (ns/day) (hour/ns) 83: Performance: 2189.266 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.1 83: (ns/day) (hour/ns) 83: Performance: 2115.589 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.3 83: (ns/day) (hour/ns) 83: Performance: 2047.389 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.1 83: (ns/day) (hour/ns) 83: Performance: 2016.561 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (5314 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.0 83: (ns/day) (hour/ns) 83: Performance: 1563.999 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.2 83: (ns/day) (hour/ns) 83: Performance: 1663.227 0.014 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.1 83: (ns/day) (hour/ns) 83: Performance: 2074.274 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.5 83: (ns/day) (hour/ns) 83: Performance: 1789.830 0.013 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 94.9 83: (ns/day) (hour/ns) 83: Performance: 1903.768 0.013 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.029 0.029 99.8 83: (ns/day) (hour/ns) 83: Performance: 50.543 0.475 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (6360 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.1 83: (ns/day) (hour/ns) 83: Performance: 1630.218 0.015 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.6 83: (ns/day) (hour/ns) 83: Performance: 1837.886 0.013 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.4 83: (ns/day) (hour/ns) 83: Performance: 2165.411 0.011 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.7 83: (ns/day) (hour/ns) 83: Performance: 2073.576 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.033 0.033 99.9 83: (ns/day) (hour/ns) 83: Performance: 44.476 0.540 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.4 83: (ns/day) (hour/ns) 83: Performance: 2086.215 0.012 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (7210 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 97.1 83: (ns/day) (hour/ns) 83: Performance: 1297.240 0.019 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.010 0.011 99.5 83: (ns/day) (hour/ns) 83: Performance: 139.200 0.172 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 4. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 4. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.8 83: (ns/day) (hour/ns) 83: Performance: 1692.471 0.014 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.033 0.033 99.9 83: (ns/day) (hour/ns) 83: Performance: 44.153 0.544 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.9 83: (ns/day) (hour/ns) 83: Performance: 1488.785 0.016 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 100. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 100. 83: 83: 83: There were 5 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.6 83: (ns/day) (hour/ns) 83: Performance: 1562.017 0.015 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (7101 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 97.4 83: (ns/day) (hour/ns) 83: Performance: 1384.092 0.017 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 97.0 83: (ns/day) (hour/ns) 83: Performance: 1481.624 0.016 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.8 83: (ns/day) (hour/ns) 83: Performance: 1654.295 0.015 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.6 83: (ns/day) (hour/ns) 83: Performance: 1473.826 0.016 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 97.2 83: (ns/day) (hour/ns) 83: Performance: 1337.515 0.018 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: NVE simulation: will use the initial temperature of 398.997 K for 83: determining the Verlet buffer size 83: 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Can not increase nstlist because an NVE ensemble is used 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.7 83: (ns/day) (hour/ns) 83: Performance: 1472.769 0.016 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (6381 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.025 0.025 99.8 83: (ns/day) (hour/ns) 83: Performance: 57.785 0.415 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.030 0.030 99.8 83: (ns/day) (hour/ns) 83: Performance: 48.288 0.497 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.021 0.021 99.7 83: (ns/day) (hour/ns) 83: Performance: 69.801 0.344 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.013 0.013 99.7 83: (ns/day) (hour/ns) 83: Performance: 111.365 0.216 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.025 0.025 99.8 83: (ns/day) (hour/ns) 83: Performance: 58.189 0.412 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 83: COM removal frequency is set to (5). 83: Other settings require a global communication frequency of 2. 83: Note that this will require additional global communication steps, 83: which will reduce performance when using multiple ranks. 83: Consider setting nstcomm to a multiple of 2. 83: 83: 83: There were 4 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.5 83: (ns/day) (hour/ns) 83: Performance: 1517.761 0.016 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (5154 ms) 83: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: This run will generate roughly 0 Mb of data 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.025 0.025 99.8 83: (ns/day) (hour/ns) 83: Performance: 57.634 0.416 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (1) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.8 83: (ns/day) (hour/ns) 83: Performance: 1383.781 0.017 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: Setting nstcalcenergy (100) equal to nstenergy (4) 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 95.8 83: (ns/day) (hour/ns) 83: Performance: 1552.178 0.015 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.001 0.001 96.0 83: (ns/day) (hour/ns) 83: Performance: 1481.981 0.016 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.021 0.021 99.7 83: (ns/day) (hour/ns) 83: Performance: 68.982 0.348 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: 83: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 83: that with the Verlet scheme, nstlist has no effect on the accuracy of 83: your simulation. 83: 83: 83: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 83: setting nstcomm equal to nstcalcenergy for less overhead 83: 83: Generated 330891 of the 330891 non-bonded parameter combinations 83: Generating 1-4 interactions: fudge = 0.5 83: 83: Generated 330891 of the 330891 1-4 parameter combinations 83: 83: Excluding 2 bonded neighbours molecule type 'SOL' 83: Number of degrees of freedom in T-Coupling group System is 27.00 83: 83: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 83: 83: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 83: 83: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 83: 83: Note that mdrun will redetermine rlist based on the actual pair-list setup 83: 83: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 83: You are using a plain Coulomb cut-off, which might produce artifacts. 83: You might want to consider using PME electrostatics. 83: 83: 83: 83: This run will generate roughly 0 Mb of data 83: 83: There were 3 NOTEs 83: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 83: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 83: 83: Using 1 MPI process 83: Using 1 OpenMP thread 83: 83: 83: NOTE: Thread affinity was not set. 83: starting mdrun 'spc2' 83: 16 steps, 0.0 ps. 83: 83: Writing final coordinates. 83: 83: Core t (s) Wall t (s) (%) 83: Time: 0.017 0.017 99.6 83: (ns/day) (hour/ns) 83: Performance: 85.507 0.281 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 83: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 83: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (6016 ms) 83: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (69340 ms total) 83: 83: [----------] Global test environment tear-down 83: [==========] 13 tests from 1 test suite ran. (69344 ms total) 83: [ PASSED ] 13 tests. 83/91 Test #83: MdrunCoordinationConstraintsTests1Rank ....... Passed 69.65 sec test 84 Start 84: MdrunCoordinationConstraintsTests2Ranks 84: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-coordination-constraints-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunCoordinationConstraintsTests2Ranks.xml" 84: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 84: Test timeout computed to be: 1920 84: [==========] Running 13 tests from 1 test suite. 84: [----------] Global test environment set-up. 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.9%. 84: The balanceable part of the MD step is 54%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: NOTE: 27 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 191.1 84: (ns/day) (hour/ns) 84: Performance: 1332.741 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.0%. 84: The balanceable part of the MD step is 51%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: NOTE: 28 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 190.1 84: (ns/day) (hour/ns) 84: Performance: 1610.402 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.0%. 84: The balanceable part of the MD step is 35%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.7%. 84: 84: 84: NOTE: 28 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.5 84: (ns/day) (hour/ns) 84: Performance: 1577.213 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.9%. 84: The balanceable part of the MD step is 34%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.6%. 84: 84: 84: NOTE: 32 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.8 84: (ns/day) (hour/ns) 84: Performance: 1652.963 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.3%. 84: The balanceable part of the MD step is 38%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.9%. 84: 84: 84: NOTE: 30 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.1 84: (ns/day) (hour/ns) 84: Performance: 1810.076 0.013 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.4%. 84: The balanceable part of the MD step is 38%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: NOTE: 30 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.001 0.001 187.7 84: (ns/day) (hour/ns) 84: Performance: 1850.028 0.013 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (7735 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.8%. 84: The balanceable part of the MD step is 53%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.4%. 84: 84: 84: NOTE: 27 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 190.8 84: (ns/day) (hour/ns) 84: Performance: 1322.867 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.7%. 84: The balanceable part of the MD step is 51%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.4%. 84: 84: 84: NOTE: 28 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.3 84: (ns/day) (hour/ns) 84: Performance: 1489.685 0.016 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.3%. 84: The balanceable part of the MD step is 45%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.6%. 84: 84: 84: NOTE: 30 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.4 84: (ns/day) (hour/ns) 84: Performance: 1656.964 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.1%. 84: The balanceable part of the MD step is 43%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.9%. 84: 84: 84: NOTE: 33 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.2 84: (ns/day) (hour/ns) 84: Performance: 1593.944 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.7%. 84: The balanceable part of the MD step is 40%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.7%. 84: 84: 84: NOTE: 33 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.5 84: (ns/day) (hour/ns) 84: Performance: 1548.082 0.016 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.2%. 84: The balanceable part of the MD step is 42%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.1%. 84: 84: 84: NOTE: 33 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.2 84: (ns/day) (hour/ns) 84: Performance: 1569.378 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (7334 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.7%. 84: The balanceable part of the MD step is 53%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.4%. 84: 84: 84: NOTE: 27 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 190.2 84: (ns/day) (hour/ns) 84: Performance: 1274.166 0.019 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.0%. 84: The balanceable part of the MD step is 48%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: NOTE: 27 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.6 84: (ns/day) (hour/ns) 84: Performance: 1477.361 0.016 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.3%. 84: The balanceable part of the MD step is 44%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.6%. 84: 84: 84: NOTE: 29 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.4 84: (ns/day) (hour/ns) 84: Performance: 1711.752 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.1%. 84: The balanceable part of the MD step is 42%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: NOTE: 33 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.6 84: (ns/day) (hour/ns) 84: Performance: 1585.126 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.7%. 84: The balanceable part of the MD step is 44%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.3%. 84: 84: 84: NOTE: 32 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.0 84: (ns/day) (hour/ns) 84: Performance: 1728.319 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.8%. 84: The balanceable part of the MD step is 41%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.3%. 84: 84: 84: NOTE: 33 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.0 84: (ns/day) (hour/ns) 84: Performance: 1556.885 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (8069 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 190.6 84: (ns/day) (hour/ns) 84: Performance: 1401.250 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.7 84: (ns/day) (hour/ns) 84: Performance: 1610.192 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.7 84: (ns/day) (hour/ns) 84: Performance: 1743.976 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.1 84: (ns/day) (hour/ns) 84: Performance: 1725.173 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.4 84: (ns/day) (hour/ns) 84: Performance: 1727.592 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 5 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.5 84: (ns/day) (hour/ns) 84: Performance: 1736.112 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (6705 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 190.0 84: (ns/day) (hour/ns) 84: Performance: 1350.563 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.4 84: (ns/day) (hour/ns) 84: Performance: 1516.454 0.016 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 8 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.5 84: (ns/day) (hour/ns) 84: Performance: 1552.960 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.2 84: (ns/day) (hour/ns) 84: Performance: 1669.764 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.058 0.029 199.6 84: (ns/day) (hour/ns) 84: Performance: 50.405 0.476 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.7 84: (ns/day) (hour/ns) 84: Performance: 1680.926 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (4354 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 190.2 84: (ns/day) (hour/ns) 84: Performance: 1365.077 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.9 84: (ns/day) (hour/ns) 84: Performance: 1592.296 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.6 84: (ns/day) (hour/ns) 84: Performance: 1810.076 0.013 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.4 84: (ns/day) (hour/ns) 84: Performance: 1688.759 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.4 84: (ns/day) (hour/ns) 84: Performance: 1723.966 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.3 84: (ns/day) (hour/ns) 84: Performance: 1769.777 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (4689 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 191.8 84: (ns/day) (hour/ns) 84: Performance: 1372.223 0.017 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 190.9 84: (ns/day) (hour/ns) 84: Performance: 1581.261 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 5 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.6 84: (ns/day) (hour/ns) 84: Performance: 1792.694 0.013 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.2 84: (ns/day) (hour/ns) 84: Performance: 1758.662 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 47 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.085 0.069 124.0 84: (ns/day) (hour/ns) 84: Performance: 21.426 1.120 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.5 84: (ns/day) (hour/ns) 84: Performance: 1754.655 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (5014 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 191.4 84: (ns/day) (hour/ns) 84: Performance: 1333.606 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.9 84: (ns/day) (hour/ns) 84: Performance: 1431.531 0.017 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.0 84: (ns/day) (hour/ns) 84: Performance: 1635.411 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.7 84: (ns/day) (hour/ns) 84: Performance: 1585.330 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.1 84: (ns/day) (hour/ns) 84: Performance: 1516.827 0.016 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 188.7 84: (ns/day) (hour/ns) 84: Performance: 1601.818 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (4315 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 191.3 84: (ns/day) (hour/ns) 84: Performance: 1302.451 0.018 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 49 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.089 0.053 169.3 84: (ns/day) (hour/ns) 84: Performance: 27.870 0.861 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 190.1 84: (ns/day) (hour/ns) 84: Performance: 1771.304 0.014 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.7 84: (ns/day) (hour/ns) 84: Performance: 1621.849 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 189.5 84: (ns/day) (hour/ns) 84: Performance: 1577.011 0.015 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.018 0.009 198.6 84: (ns/day) (hour/ns) 84: Performance: 162.352 0.148 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (3242 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.5%. 84: The balanceable part of the MD step is 60%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.3%. 84: 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 187.9 84: (ns/day) (hour/ns) 84: Performance: 904.042 0.027 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 4 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.1%. 84: The balanceable part of the MD step is 60%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.6%. 84: 84: 84: NOTE: 8 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 188.3 84: (ns/day) (hour/ns) 84: Performance: 1036.526 0.023 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 4. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 4. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.4%. 84: The balanceable part of the MD step is 47%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.7%. 84: 84: 84: NOTE: 5 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 187.1 84: (ns/day) (hour/ns) 84: Performance: 1144.135 0.021 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.1%. 84: The balanceable part of the MD step is 46%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 185.3 84: (ns/day) (hour/ns) 84: Performance: 1149.794 0.021 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.7%. 84: The balanceable part of the MD step is 45%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.3%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 185.8 84: (ns/day) (hour/ns) 84: Performance: 1191.835 0.020 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 100. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 100. 84: 84: 84: There were 5 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.2%. 84: The balanceable part of the MD step is 45%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.5%. 84: 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 186.2 84: (ns/day) (hour/ns) 84: Performance: 1146.264 0.021 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (4798 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 0.6%. 84: The balanceable part of the MD step is 59%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.3%. 84: 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 188.6 84: (ns/day) (hour/ns) 84: Performance: 915.461 0.026 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.0%. 84: The balanceable part of the MD step is 59%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 0.6%. 84: 84: 84: NOTE: 8 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 188.0 84: (ns/day) (hour/ns) 84: Performance: 1046.030 0.023 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.8%. 84: The balanceable part of the MD step is 55%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.0%. 84: 84: 84: NOTE: 8 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 186.8 84: (ns/day) (hour/ns) 84: Performance: 1084.803 0.022 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.0%. 84: The balanceable part of the MD step is 52%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.0%. 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE: 8 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.023 11.2 84: (ns/day) (hour/ns) 84: Performance: 62.846 0.382 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 1.9%. 84: The balanceable part of the MD step is 52%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.0%. 84: 84: 84: NOTE: 85 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.123 0.062 199.5 84: (ns/day) (hour/ns) 84: Performance: 23.848 1.006 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: NVE simulation: will use the initial temperature of 398.997 K for 84: determining the Verlet buffer size 84: 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.779 nm, buffer size 0.079 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.773 nm, buffer size 0.073 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Can not increase nstlist because an NVE ensemble is used 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: 84: Dynamic load balancing report: 84: DLB was off during the run due to low measured imbalance. 84: Average load imbalance: 2.2%. 84: The balanceable part of the MD step is 50%, load imbalance is computed from this. 84: Part of the total run time spent waiting due to load imbalance: 1.1%. 84: 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 186.9 84: (ns/day) (hour/ns) 84: Performance: 1021.149 0.024 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (3591 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 40 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.198 0.099 199.7 84: (ns/day) (hour/ns) 84: Performance: 14.835 1.618 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 186.3 84: (ns/day) (hour/ns) 84: Performance: 1005.483 0.024 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 6 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 185.2 84: (ns/day) (hour/ns) 84: Performance: 1140.534 0.021 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 5 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 184.0 84: (ns/day) (hour/ns) 84: Performance: 1078.913 0.022 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 5 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 184.6 84: (ns/day) (hour/ns) 84: Performance: 1113.126 0.022 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]: 84: COM removal frequency is set to (5). 84: Other settings require a global communication frequency of 2. 84: Note that this will require additional global communication steps, 84: which will reduce performance when using multiple ranks. 84: Consider setting nstcomm to a multiple of 2. 84: 84: 84: There were 4 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 5 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.002 0.001 184.5 84: (ns/day) (hour/ns) 84: Performance: 1120.108 0.021 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (5302 ms) 84: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.002 186.6 84: (ns/day) (hour/ns) 84: Performance: 937.900 0.026 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (1) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 186.2 84: (ns/day) (hour/ns) 84: Performance: 988.066 0.024 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 16 time 0.016 Last energy frame read 16 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: Setting nstcalcenergy (100) equal to nstenergy (4) 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: There were 3 NOTEs 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: This run will generate roughly 0 Mb of data 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 185.9 84: (ns/day) (hour/ns) 84: Performance: 1069.919 0.022 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Last energy frame read 4 time 0.016 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 184.9 84: (ns/day) (hour/ns) 84: Performance: 995.249 0.024 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 184.9 84: (ns/day) (hour/ns) 84: Performance: 1040.026 0.023 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: 84: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 84: that with the Verlet scheme, nstlist has no effect on the accuracy of 84: your simulation. 84: 84: 84: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, consider 84: setting nstcomm equal to nstcalcenergy for less overhead 84: 84: Generated 330891 of the 330891 non-bonded parameter combinations 84: Generating 1-4 interactions: fudge = 0.5 84: 84: Generated 330891 of the 330891 1-4 parameter combinations 84: 84: Excluding 2 bonded neighbours molecule type 'SOL' 84: Number of degrees of freedom in T-Coupling group System is 27.00 84: 84: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 84: 84: Calculated rlist for 1x1 atom pair-list as 0.768 nm, buffer size 0.068 nm 84: 84: Set rlist, assuming 4x4 atom pair-list, to 0.762 nm, buffer size 0.062 nm 84: 84: Note that mdrun will redetermine rlist based on the actual pair-list setup 84: 84: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]: 84: You are using a plain Coulomb cut-off, which might produce artifacts. 84: You might want to consider using PME electrostatics. 84: 84: 84: 84: This run will generate roughly 0 Mb of data 84: 84: There were 3 NOTEs 84: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 84: Changing nstlist from 8 to 20, rlist from 0.762 to 0.876 84: 84: Using 2 MPI processes 84: Using 1 OpenMP thread per MPI process 84: 84: 84: NOTE: The number of threads is not equal to the number of (logical) cpus 84: and the -pin option is set to auto: will not pin threads to cpus. 84: This can lead to significant performance degradation. 84: Consider using -pin on (and -pinoffset in case you run multiple jobs). 84: starting mdrun 'spc2' 84: 16 steps, 0.0 ps. 84: 84: Writing final coordinates. 84: 84: NOTE: 7 % of the run time was spent communicating energies, 84: you might want to increase some nst* mdp options 84: 84: Core t (s) Wall t (s) (%) 84: Time: 0.003 0.001 185.0 84: (ns/day) (hour/ns) 84: Performance: 1012.257 0.024 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file 84: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file 84: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (6111 ms) 84: [----------] 13 tests from PropagatorsWithConstraints/PeriodicActionsTest (71419 ms total) 84: 84: [----------] Global test environment tear-down 84: [==========] 13 tests from 1 test suite ran. (71467 ms total) 84: [ PASSED ] 13 tests. 84/91 Test #84: MdrunCoordinationConstraintsTests2Ranks ...... Passed 72.03 sec test 85 Start 85: MdrunFEPTests 85: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-fep-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunFEPTests.xml" 85: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 85: Test timeout computed to be: 600 85: [==========] Running 12 tests from 1 test suite. 85: [----------] Global test environment set-up. 85: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp, line 149]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_coul/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -34746470 85: 85: Generated 153 of the 153 non-bonded parameter combinations 85: 85: Generated 153 of the 153 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 4.080 2.040 200.0 85: (ns/day) (hour/ns) 85: Performance: 0.889 26.988 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_coul_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 trr version: GMX_trn_file (single precision) 85: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_coul_s (53678 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp, line 148]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwsequential_vdw/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to 2117853174 85: 85: Generated 153 of the 153 non-bonded parameter combinations 85: 85: Generated 153 of the 153 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 4.027 2.014 200.0 85: (ns/day) (hour/ns) 85: Performance: 0.901 26.637 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwsequential_vdw_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwsequential_vdw_s (2644 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp, line 147]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 4 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -1581389833 85: 85: Generated 153 of the 153 non-bonded parameter combinations 85: 85: Generated 153 of the 153 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.216 1.108 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.637 14.657 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_s (1669 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp, line 147]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 3 [file topol.top, line 155]: 85: System has non-zero total charge: 1.000000 85: Total charge should normally be an integer. See 85: https://manual.gromacs.org/current/user-guide/floating-point.html 85: for discussion on how close it should be to an integer. 85: 85: 85: 85: 85: WARNING 2 [file topol.top, line 155]: 85: You are using Ewald electrostatics in a system with net charge. This can 85: lead to severe artifacts, such as ions moving into regions with low 85: dielectric, due to the uniform background charge. We suggest to 85: neutralize your system with counter ions, possibly in combination with a 85: physiological salt concentration. 85: 85: Setting the LD random seed to -1119903756 85: 85: Generated 171 of the 171 non-bonded parameter combinations 85: 85: Generated 171 of the 171 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Excluding 1 bonded neighbours molecule type 'NA' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: 85: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 85: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 85: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 85: Charge 85: J. Chem. Theory Comput. 10 (2014) pp. 381-393 85: -------- -------- --- Thank You --- -------- -------- 85: 85: Number of degrees of freedom in T-Coupling group System is 358.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-net-charge/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 5 NOTEs 85: 85: There were 2 WARNINGs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 50, rlist from 1.004 to 1.101 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: There are: 1 Ion residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 85: 85: Estimate for the relative computational load of the PME mesh part: 0.96 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.800 1.400 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.296 18.518 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_net_charge_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_net_charge_s (81442 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp, line 147]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: NOTE 3 [file topol.top, line 165]: 85: System has non-zero total charge: 1.000000 85: Total charge should normally be an integer. See 85: https://manual.gromacs.org/current/user-guide/floating-point.html 85: for discussion on how close it should be to an integer. 85: 85: 85: 85: 85: WARNING 2 [file topol.top, line 165]: 85: You are using Ewald electrostatics in a system with net charge. This can 85: lead to severe artifacts, such as ions moving into regions with low 85: dielectric, due to the uniform background charge. We suggest to 85: neutralize your system with counter ions, possibly in combination with a 85: physiological salt concentration. 85: 85: Setting the LD random seed to -536891395 85: 85: Generated 190 of the 190 non-bonded parameter combinations 85: 85: Generated 190 of the 190 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Excluding 1 bonded neighbours molecule type 'NA' 85: 85: turning H bonds into constraints... 85: 85: Excluding 1 bonded neighbours molecule type 'CL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'CL' 85: 85: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 85: J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof 85: Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net 85: Charge 85: J. Chem. Theory Comput. 10 (2014) pp. 381-393 85: -------- -------- --- Thank You --- -------- -------- 85: 85: Number of degrees of freedom in T-Coupling group System is 361.00 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/coulandvdwtogether-decouple-counter-charge/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 5 NOTEs 85: 85: There were 2 WARNINGs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 50, rlist from 1.004 to 1.102 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: There are: 2 Ion residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 85: 85: Determining Verlet buffer for a tolerance of 5e-05 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.004 nm, buffer size 0.004 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 32x32x32, spacing 0.095 0.095 0.095 85: 85: Estimate for the relative computational load of the PME mesh part: 0.96 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.776 1.388 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.307 18.362 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_coulandvdwtogether_decouple_counter_charge_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/coulandvdwtogether_decouple_counter_charge_s (1537 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp, line 171]: 85: For proper sampling of the (nearly) decoupled state, stochastic dynamics 85: should be used 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 85: Replacing vdwtype=Shift by the equivalent combination of vdwtype=Cut-off 85: and vdw_modifier=Force-switch 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/expanded/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 4 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 100 steps, 0.1 ps. 85: Setting the LD random seed to 1070542739 85: 85: Generated 153 of the 153 non-bonded parameter combinations 85: 85: Generated 153 of the 153 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: 85: Coupling 1 copies of molecule type 'ASN' 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 14.236 7.118 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.226 19.577 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_expanded_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Reading energy frame 30 time 0.030 Reading energy frame 40 time 0.040 Reading energy frame 50 time 0.050 Reading energy frame 60 time 0.060 Reading energy frame 70 time 0.070 Reading energy frame 80 time 0.080 Reading energy frame 90 time 0.090 Reading energy frame 100 time 0.100 Last energy frame read 100 time 0.100 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/expanded_s (7645 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: WARNING 2 [file topol.top, line 72]: 85: No default Bond types for perturbed atoms, using normal values 85: 85: 85: WARNING 3 [file topol.top, line 73]: 85: No default Bond types for perturbed atoms, using normal values 85: 85: 85: WARNING 4 [file topol.top, line 98]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 5 [file topol.top, line 99]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 6 [file topol.top, line 100]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 7 [file topol.top, line 101]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 8 [file topol.top, line 111]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 9 [file topol.top, line 112]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 10 [file topol.top, line 113]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 11 [file topol.top, line 114]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 2 NOTEs 85: 85: There were 11 WARNINGs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -8921114 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.95 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 4.210 2.105 200.0 85: (ns/day) (hour/ns) 85: Performance: 0.862 27.843 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_s (2497 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: 85: WARNING 2 [file topol.top, line 72]: 85: No default Bond types for perturbed atoms, using normal values 85: 85: 85: WARNING 3 [file topol.top, line 73]: 85: No default Bond types for perturbed atoms, using normal values 85: 85: 85: WARNING 4 [file topol.top, line 98]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 5 [file topol.top, line 99]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 6 [file topol.top, line 100]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 7 [file topol.top, line 101]: 85: No default Angle types for perturbed atoms, using normal values 85: 85: 85: WARNING 8 [file topol.top, line 111]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 9 [file topol.top, line 112]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 10 [file topol.top, line 113]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: 85: WARNING 11 [file topol.top, line 114]: 85: No default Ryckaert-Bell. types for perturbed atoms, using normal values 85: 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 85: Removing center of mass motion in the presence of position restraints 85: might cause artifacts. When you are using position restraints to 85: equilibrate a macro-molecule, the artifacts are usually negligible. 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/relative-position-restraints/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There were 11 WARNINGs 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -985964609 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.94 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 3.310 1.655 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.096 21.896 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_relative_position_restraints_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/relative_position_restraints_s (2197 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/restraints/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 2 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -403939538 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.331 nm between atom 1 and 9 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.89 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.342 0.671 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.705 8.874 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_restraints_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/restraints_s (993 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/simtemp/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: There was 1 NOTE 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.677 0.839 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.163 11.095 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_simtemp_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 Setting the LD random seed to -1129252897 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between excluded atoms is 0.331 nm between atom 1 and 9 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.90 85: 85: This run will generate roughly 0 Mb of data 85: [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/simtemp_s (1233 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/transformAtoB/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -677642373 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.164 nm between atom 41 and 42 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.95 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 2.851 1.425 200.0 85: (ns/day) (hour/ns) 85: Performance: 1.273 18.854 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_transformAtoB_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/transformAtoB_s (1844 ms) 85: [ RUN ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s 85: 85: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 85: With PME there is a minor soft core effect present at the cut-off, 85: proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on 85: energy conservation, but usually other effects dominate. With a common 85: sigma value of 0.34 nm the fraction of the particle-particle potential at 85: the cut-off at lambda=0.5 is around 6.4e-05, while ewald-rtol is 1.0e-06. 85: 85: 85: WARNING 1 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 85: The Berendsen thermostat does not generate the correct kinetic energy 85: distribution, and should not be used for new production simulations (in 85: our opinion). We would recommend the V-rescale thermostat. 85: 85: Generating 1-4 interactions: fudge = 0.5 85: Number of degrees of freedom in T-Coupling group System is 355.00 85: 85: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 85: The optimal PME mesh load for parallel simulations is below 0.5 85: and for highly parallel simulations between 0.25 and 0.33, 85: for higher performance, increase the cut-off and the PME grid spacing. 85: 85: 85: 85: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/freeenergy/vdwalone/grompp.mdp]: 85: For free energy simulations, the optimal load limit increases from 0.5 to 85: 0.667 85: 85: 85: 85: There were 3 NOTEs 85: 85: There was 1 WARNING 85: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_sim.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 85: Changing nstlist from 10 to 100, rlist from 1 to 1 85: 85: Using 1 MPI process 85: Using 2 OpenMP threads 85: 85: 85: NOTE: The number of threads is not equal to the number of (logical) cpus 85: and the -pin option is set to auto: will not pin threads to cpus. 85: This can lead to significant performance degradation. 85: Consider using -pin on (and -pinoffset in case you run multiple jobs). 85: starting mdrun 'AA' 85: 20 steps, 0.0 ps. 85: Setting the LD random seed to -67305890 85: 85: Generated 136 of the 136 non-bonded parameter combinations 85: 85: Generated 136 of the 136 1-4 parameter combinations 85: 85: Excluding 3 bonded neighbours molecule type 'ASN' 85: 85: turning H bonds into constraints... 85: 85: Excluding 2 bonded neighbours molecule type 'SOL' 85: 85: turning H bonds into constraints... 85: Analysing residue names: 85: There are: 1 Protein residues 85: There are: 56 Water residues 85: Analysing Protein... 85: 85: The largest distance between non-perturbed excluded atoms is 0.172 nm between atom 8 and 9 85: 85: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 85: 85: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 85: 85: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 85: 85: Note that mdrun will redetermine rlist based on the actual pair-list setup 85: Calculating fourier grid dimensions for X Y Z 85: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 85: 85: Estimate for the relative computational load of the PME mesh part: 0.90 85: 85: This run will generate roughly 0 Mb of data 85: 85: Writing final coordinates. 85: 85: Core t (s) Wall t (s) (%) 85: Time: 1.729 0.865 200.0 85: (ns/day) (hour/ns) 85: Performance: 2.099 11.436 85: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/EquivalentToReference_FreeEnergyReferenceTest_WithinTolerances_vdwalone_s_energy.edr as single precision energy file 85: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 Reading energy frame 2 time 0.002 Reading energy frame 3 time 0.003 Reading energy frame 4 time 0.004 Reading energy frame 5 time 0.005 Reading energy frame 6 time 0.006 Reading energy frame 7 time 0.007 Reading energy frame 8 time 0.008 Reading energy frame 9 time 0.009 Reading energy frame 10 time 0.010 Reading energy frame 11 time 0.011 Reading energy frame 12 time 0.012 Reading energy frame 13 time 0.013 Reading energy frame 14 time 0.014 Reading energy frame 15 time 0.015 Reading energy frame 16 time 0.016 Reading energy frame 17 time 0.017 Reading energy frame 18 time 0.018 Reading energy frame 19 time 0.019 Reading energy frame 20 time 0.020 Last energy frame read 20 time 0.020 [ OK ] EquivalentToReference/FreeEnergyReferenceTest.WithinTolerances/vdwalone_s (1219 ms) 85: [----------] 12 tests from EquivalentToReference/FreeEnergyReferenceTest (158604 ms total) 85: 85: [----------] Global test environment tear-down 85: [==========] 12 tests from 1 test suite ran. (158620 ms total) 85: [ PASSED ] 12 tests. 85/91 Test #85: MdrunFEPTests ................................ Passed 158.84 sec test 86 Start 86: MdrunPullTests 86: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-pull-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunPullTests.xml" 86: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 86: Test timeout computed to be: 600 86: [==========] Running 4 tests from 1 test suite. 86: [----------] Global test environment set-up. 86: [----------] 4 tests from PullTest/PullIntegrationTest 86: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/0 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'r_1' has 3 atoms 86: Pull group 2 'r_2' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 1293.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0_input.mdp]: 86: NVE simulation: will use the initial temperature of 303.122 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 0.575 nm 0.600 nm 86: 86: There was 1 NOTE 86: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.420 0.210 199.9 86: (ns/day) (hour/ns) 86: Performance: 8.634 2.780 86: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_0.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/0 (1065 ms) 86: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/1 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'r_1' has 3 atoms 86: Pull group 2 'r_2' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 1293.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1_input.mdp]: 86: NVE simulation: will use the initial temperature of 303.122 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 0.301 nm 0.400 nm 86: 86: There was 1 NOTE 86: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.602 0.301 200.0 86: (ns/day) (hour/ns) 86: Performance: 6.030 3.980 86: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_1.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/1 (988 ms) 86: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/2 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'r_1' has 3 atoms 86: Pull group 2 'r_2' has 3 atoms 86: Pull group 3 'r_3' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 1292.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2_input.mdp]: 86: NVE simulation: will use the initial temperature of 303.357 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 0.575 nm 0.500 nm 86: 1 3 2 86: 3 3 8 0.331 nm 0.400 nm 86: 86: There was 1 NOTE 86: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.357 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: NOTE: 14 % of the run time was spent in pair search, 86: you might want to increase nstlist (this has no effect on accuracy) 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.478 0.239 199.9 86: (ns/day) (hour/ns) 86: Performance: 7.584 3.165 86: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_2.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/2 (992 ms) 86: [ RUN ] PullTest/PullIntegrationTest.WithinTolerances/3 86: Generating 1-4 interactions: fudge = 0.5 86: Pull group 1 'r_1' has 3 atoms 86: Pull group 2 'r_2' has 3 atoms 86: Number of degrees of freedom in T-Coupling group System is 1293.00 86: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 86: 86: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3_input.mdp]: 86: NVE simulation: will use the initial temperature of 303.122 K for 86: determining the Verlet buffer size 86: 86: Pull group natoms pbc atom distance at start reference at t=0 86: 1 3 2 86: 2 3 5 0.575 nm 0.000 nm 86: 1 3 2 86: 2 3 5 0.050 nm 0.000 nm 86: 86: There was 1 NOTE 86: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 86: Can not increase nstlist because an NVE ensemble is used 86: Using 1 MPI process 86: Using 2 OpenMP threads 86: 86: 86: NOTE: The number of threads is not equal to the number of (logical) cpus 86: and the -pin option is set to auto: will not pin threads to cpus. 86: This can lead to significant performance degradation. 86: Consider using -pin on (and -pinoffset in case you run multiple jobs). 86: starting mdrun 'spc2' 86: 20 steps, 0.0 ps. 86: Generated 330891 of the 330891 non-bonded parameter combinations 86: 86: Generated 330891 of the 330891 1-4 parameter combinations 86: 86: Excluding 2 bonded neighbours molecule type 'SOL' 86: 86: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 303.122 K 86: 86: Calculated rlist for 1x1 atom pair-list as 0.781 nm, buffer size 0.081 nm 86: 86: Set rlist, assuming 4x4 atom pair-list, to 0.772 nm, buffer size 0.072 nm 86: 86: Note that mdrun will redetermine rlist based on the actual pair-list setup 86: 86: This run will generate roughly 0 Mb of data 86: 86: Writing final coordinates. 86: 86: Core t (s) Wall t (s) (%) 86: Time: 0.544 0.272 199.9 86: (ns/day) (hour/ns) 86: Performance: 6.670 3.598 86: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/PullTest_PullIntegrationTest_WithinTolerances_3.edr as single precision energy file 86: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.005 Reading energy frame 2 time 0.010 Reading energy frame 3 time 0.015 Reading energy frame 4 time 0.020 Last energy frame read 4 time 0.020 [ OK ] PullTest/PullIntegrationTest.WithinTolerances/3 (823 ms) 86: [----------] 4 tests from PullTest/PullIntegrationTest (3869 ms total) 86: 86: [----------] Global test environment tear-down 86: [==========] 4 tests from 1 test suite ran. (3881 ms total) 86: [ PASSED ] 4 tests. 86/91 Test #86: MdrunPullTests ............................... Passed 4.11 sec test 87 Start 87: MdrunRotationTests 87: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-rotation-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunRotationTests.xml" 87: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 87: Test timeout computed to be: 600 87: [==========] Running 12 tests from 1 test suite. 87: [----------] Global test environment set-up. 87: [----------] 12 tests from RotationWorks/RotationTest 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 87: Enforced rotation: Group 0 (iso) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: trr version: GMX_trn_file (single precision) 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -26608258 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 15 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.594 0.297 200.0 87: (ns/day) (hour/ns) 87: Performance: 15.130 1.586 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_0.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/0 (328 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 87: Enforced rotation: Group 0 (iso-pf) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -553713794 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.040 0.020 199.4 87: (ns/day) (hour/ns) 87: Performance: 223.582 0.107 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_1.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/1 (87 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 87: Enforced rotation: Group 0 (pm) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -5096449 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 17 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.520 0.260 200.0 87: (ns/day) (hour/ns) 87: Performance: 17.273 1.389 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_2.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/2 (321 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 87: Enforced rotation: Group 0 (pm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to 536346236 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 10 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.580 0.290 200.0 87: (ns/day) (hour/ns) 87: Performance: 15.502 1.548 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_3.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/3 (330 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 87: Enforced rotation: Group 0 (rm) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -86035466 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 13 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.526 0.263 199.9 87: (ns/day) (hour/ns) 87: Performance: 17.094 1.404 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_4.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/4 (291 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 87: Enforced rotation: Group 0 (rm-pf) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -1497699841 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 16 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.562 0.281 200.0 87: (ns/day) (hour/ns) 87: Performance: 15.974 1.502 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_5.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/5 (339 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 87: Enforced rotation: Group 0 (rm2) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -1311058 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 13 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.369 0.185 199.9 87: (ns/day) (hour/ns) 87: Performance: 24.312 0.987 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_6.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/6 (209 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 87: Enforced rotation: Group 0 (rm2-pf) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -1295257953 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 15 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.422 0.211 199.9 87: (ns/day) (hour/ns) 87: Performance: 21.289 1.127 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_7.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/7 (227 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 87: Enforced rotation: Group 0 (flex) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -6345729 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 22 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.462 0.231 199.9 87: (ns/day) (hour/ns) 87: Performance: 19.441 1.235 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_8.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/8 (251 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 87: Enforced rotation: Group 0 (flex-t) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -562302225 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 13 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.364 0.182 199.9 87: (ns/day) (hour/ns) 87: Performance: 24.683 0.972 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_9.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/9 (198 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 87: Enforced rotation: Group 0 (flex2) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to -755450369 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.365 0.183 199.9 87: (ns/day) (hour/ns) 87: Performance: 24.581 0.976 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_10.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/10 (207 ms) 87: [ RUN ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 87: Enforced rotation: Group 0 (flex2-t) normalized rot. vector: 0.267261 0.534522 0.801784 87: 87: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 87: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 87: that with the Verlet scheme, nstlist has no effect on the accuracy of 87: your simulation. 87: 87: Rotation group 0 'system' has 4 atoms 87: Number of degrees of freedom in T-Coupling group rest is 9.00 87: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 87: 87: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11_input.mdp]: 87: NVE simulation with an initial temperature of zero: will use a Verlet 87: buffer of 10%. Check your energy drift! 87: 87: Enforced rotation: group 0 has 4 reference positions. 87: Reading them from /build/reproducible-path/gromacs-2024.4/src/testutils/simulationdatabase/rotref.0.trr. 87: 87: There were 2 NOTEs 87: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 87: Can not increase nstlist because an NVE ensemble is used 87: Using 1 MPI process 87: Using 2 OpenMP threads 87: 87: 87: NOTE: The number of threads is not equal to the number of (logical) cpus 87: and the -pin option is set to auto: will not pin threads to cpus. 87: This can lead to significant performance degradation. 87: Consider using -pin on (and -pinoffset in case you run multiple jobs). 87: starting mdrun 'Good gRace! Old Maple Actually Chews Slate' 87: 25 steps, 0.1 ps. 87: Setting the LD random seed to 2042621951 87: 87: Generated 1 of the 1 non-bonded parameter combinations 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonA' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonB' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonC' 87: 87: Excluding 1 bonded neighbours molecule type 'ArgonD' 87: 87: This run will generate roughly 0 Mb of data 87: 87: Writing final coordinates. 87: 87: NOTE: 17 % of the run time was spent in pair search, 87: you might want to increase nstlist (this has no effect on accuracy) 87: 87: Core t (s) Wall t (s) (%) 87: Time: 0.305 0.153 199.9 87: (ns/day) (hour/ns) 87: Performance: 29.438 0.815 87: Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Opened /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/RotationWorks_RotationTest_CheckEnergiesForcesAndTraj_11.edr as single precision energy file 87: Reading energy frame 0 time 0.002 Reading energy frame 1 time 0.012 Reading energy frame 2 time 0.022 Reading energy frame 3 time 0.032 Reading energy frame 4 time 0.042 Reading energy frame 5 time 0.052 Last energy frame read 5 time 0.052 87: [ OK ] RotationWorks/RotationTest.CheckEnergiesForcesAndTraj/11 (170 ms) 87: [----------] 12 tests from RotationWorks/RotationTest (2964 ms total) 87: 87: [----------] Global test environment tear-down 87: [==========] 12 tests from 1 test suite ran. (2976 ms total) 87: [ PASSED ] 12 tests. 87/91 Test #87: MdrunRotationTests ........................... Passed 3.16 sec test 88 Start 88: MdrunSimulatorComparison 88: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-simulator-comparison-test "-ntomp" "2" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunSimulatorComparison.xml" 88: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 88: Test timeout computed to be: 600 88: [==========] Running 0 tests from 0 test suites. 88: [==========] 0 tests from 0 test suites ran. (0 ms total) 88: [ PASSED ] 0 tests. 88: 88: YOU HAVE 82 DISABLED TESTS 88: 88/91 Test #88: MdrunSimulatorComparison ..................... Passed 0.16 sec test 89 Start 89: MdrunVirtualSiteTests 89: Test command: /usr/bin/mpiexec "-n" "2" "/build/reproducible-path/gromacs-2024.4/build/mpi/bin/mdrun-vsites-test" "--gtest_output=xml:/build/reproducible-path/gromacs-2024.4/build/mpi/Testing/Temporary/MdrunVirtualSiteTests.xml" 89: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests 89: Test timeout computed to be: 600 89: [==========] Running 37 tests from 2 test suites. 89: [----------] Global test environment set-up. 89: [----------] 1 test from VirtualSiteVelocityTest 89: [ RUN ] VirtualSiteVelocityTest.ReferenceIsCorrect 89: [ OK ] VirtualSiteVelocityTest.ReferenceIsCorrect (0 ms) 89: [----------] 1 test from VirtualSiteVelocityTest (8 ms total) 89: 89: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 83.9%. 89: The balanceable part of the MD step is 33%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 27.8%. 89: 89: NOTE: 27.8 % of the available CPU time was lost due to load imbalance 89: in the domain decomposition. 89: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 89: You can also consider manually changing the decomposition (option -dd); 89: e.g. by using fewer domains along the box dimension in which there is 89: considerable inhomogeneity in the simulated system. 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: trr version: GMX_trn_file (single precision) 89: 89: 89: NOTE: 22 % of the run time was spent in domain decomposition, 89: 0 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 19 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.448 0.253 177.1 89: (ns/day) (hour/ns) 89: Performance: 3.074 7.808 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_0.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: trr version: GMX_trn_file (single precision) 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/0 (660 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 70.8%. 89: The balanceable part of the MD step is 31%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 22.3%. 89: 89: NOTE: 22.3 % of the available CPU time was lost due to load imbalance 89: in the domain decomposition. 89: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 89: You can also consider manually changing the decomposition (option -dd); 89: e.g. by using fewer domains along the box dimension in which there is 89: considerable inhomogeneity in the simulated system. 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: 89: NOTE: 24 % of the run time was spent in domain decomposition, 89: 0 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 21 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.469 0.253 185.6 89: (ns/day) (hour/ns) 89: Performance: 3.074 7.807 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_1.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/1 (676 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 72.9%. 89: The balanceable part of the MD step is 30%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 21.7%. 89: 89: NOTE: 21.7 % of the available CPU time was lost due to load imbalance 89: in the domain decomposition. 89: Dynamic load balancing was automatically disabled, but it might be beneficial to manually turn it on (option -dlb yes.) 89: You can also consider manually changing the decomposition (option -dd); 89: e.g. by using fewer domains along the box dimension in which there is 89: considerable inhomogeneity in the simulated system. 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: 89: NOTE: 22 % of the run time was spent in domain decomposition, 89: 0 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 21 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.592 0.312 189.8 89: (ns/day) (hour/ns) 89: Performance: 2.492 9.629 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_2.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/2 (736 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: 89: NOTE: 12 % of the run time was spent in domain decomposition, 89: 0 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 21 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.291 0.159 182.5 89: (ns/day) (hour/ns) 89: Performance: 4.875 4.923 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_3.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/3 (592 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: 89: NOTE: 13 % of the run time was spent in domain decomposition, 89: 0 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 21 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.532 0.280 190.0 89: (ns/day) (hour/ns) 89: Performance: 2.778 8.638 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_4.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/4 (787 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: 89: NOTE: 15 % of the run time was spent in domain decomposition, 89: 0 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 19 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.520 0.278 187.1 89: (ns/day) (hour/ns) 89: Performance: 2.799 8.575 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_5.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/5 (801 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 18 % of the run time was spent in domain decomposition, 89: 0 % of the run time was spent in pair search, 89: you might want to increase nstlist (this has no effect on accuracy) 89: 89: NOTE: 18 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.333 0.166 199.9 89: (ns/day) (hour/ns) 89: Performance: 4.675 5.134 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_6.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/6 (607 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.001 0.001 186.8 89: (ns/day) (hour/ns) 89: Performance: 1002.610 0.024 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_7.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/7 (52 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 89: 1 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 5 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 5 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 29 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.5 89: (ns/day) (hour/ns) 89: Performance: 817.314 0.029 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_8.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/8 (160 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Reading virtual site types... 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: The integrator does not provide a ensemble temperature, there is no system ensemble temperature 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 8.3%. 89: The balanceable part of the MD step is 37%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 3.1%. 89: 89: 89: NOTE: 29 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.7 89: (ns/day) (hour/ns) 89: Performance: 888.085 0.027 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_9.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/9 (70 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 89: NVE simulation with an initial temperature of zero: will use a Verlet 89: buffer of 10%. Check your energy drift! 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Can not increase nstlist because an NVE ensemble is used 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: 89: Dynamic load balancing report: 89: DLB was off during the run due to low measured imbalance. 89: Average load imbalance: 6.2%. 89: The balanceable part of the MD step is 40%, load imbalance is computed from this. 89: Part of the total run time spent waiting due to load imbalance: 2.5%. 89: 89: 89: NOTE: 29 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.4 89: (ns/day) (hour/ns) 89: Performance: 878.161 0.027 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_10.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/10 (33 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/11 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 96 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.032 0.022 145.7 89: (ns/day) (hour/ns) 89: Performance: 35.021 0.685 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_12.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: Reading virtual site types... 89: 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/12 (103 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 187.3 89: (ns/day) (hour/ns) 89: Performance: 954.071 0.025 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_13.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/13 (90 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/14 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 30 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 189.0 89: (ns/day) (hour/ns) 89: Performance: 874.394 0.027 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_15.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/15 (70 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 30 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.3 89: (ns/day) (hour/ns) 89: Performance: 858.400 0.028 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_16.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/16 (105 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/17 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: There were 4 NOTEs 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: This run will generate roughly 0 Mb of data 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.001 0.001 188.7 89: (ns/day) (hour/ns) 89: Performance: 979.133 0.025 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_18.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/18 (131 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 29 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 188.6 89: (ns/day) (hour/ns) 89: Performance: 884.352 0.027 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_19.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/19 (69 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.715 nm, buffer size 0.015 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.712 nm, buffer size 0.012 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 50, rlist from 0.712 to 0.801 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 187.9 89: (ns/day) (hour/ns) 89: Performance: 959.968 0.025 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_20.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/20 (74 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/21 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/22 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/23 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/24 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/25 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/26 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 30 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.001 0.001 188.3 89: (ns/day) (hour/ns) 89: Performance: 1017.785 0.024 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_27.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: Reading virtual site types... 89: 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/27 (67 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 31 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 187.7 89: (ns/day) (hour/ns) 89: Performance: 965.795 0.025 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading virtual site types... 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_28.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/28 (76 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 89: 89: NOTE 1 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 89: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 89: that with the Verlet scheme, nstlist has no effect on the accuracy of 89: your simulation. 89: 89: 89: NOTE 2 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 89: Setting nstcalcenergy (100) equal to nstenergy (4) 89: 89: Generated 3 of the 6 non-bonded parameter combinations 89: 89: Excluding 3 bonded neighbours molecule type 'VSTEST' 89: 89: Cleaning up constraints and constant bonded interactions with virtual sites 89: Number of degrees of freedom in T-Coupling group System is 45.00 89: 89: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 89: 89: NOTE 3 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 89: There are 6 non-linear virtual site constructions. Their contribution to 89: the energy error is approximated. In most cases this does not affect the 89: error significantly. 89: 89: 89: Calculated rlist for 1x1 atom pair-list as 0.732 nm, buffer size 0.032 nm 89: 89: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm 89: 89: Note that mdrun will redetermine rlist based on the actual pair-list setup 89: 89: NOTE 4 [file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29_input.mdp]: 89: You are using a plain Coulomb cut-off, which might produce artifacts. 89: You might want to consider using PME electrostatics. 89: 89: 89: 89: This run will generate roughly 0 Mb of data 89: 89: There were 4 NOTEs 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805 89: 89: Update groups can not be used for this system because an incompatible virtual site type is used 89: 89: Using 2 MPI processes 89: Using 1 OpenMP thread per MPI process 89: 89: 89: NOTE: The number of threads is not equal to the number of (logical) cpus 89: and the -pin option is set to auto: will not pin threads to cpus. 89: This can lead to significant performance degradation. 89: Consider using -pin on (and -pinoffset in case you run multiple jobs). 89: starting mdrun 'Virtual sites test system in vacuo' 89: 8 steps, 0.0 ps. 89: 89: Writing final coordinates. 89: 89: NOTE: 30 % of the run time was spent communicating energies, 89: you might want to increase some nst* mdp options 89: 89: Core t (s) Wall t (s) (%) 89: Time: 0.002 0.001 187.7 89: (ns/day) (hour/ns) 89: Performance: 952.677 0.025 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: Reading file /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/mdrun/tests/Testing/Temporary/VelocitiesConformToExpectations_VirtualSiteTest_WithinToleranceOfReference_29.tpr, VERSION 2024.4-Debian_2024.4_1 (single precision) 89: 89: Reading virtual site types... 89: Reading virtual site types... 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/29 (58 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/30 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/31 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/32 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/33 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/34 (0 ms) 89: [ RUN ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 89: [ OK ] VelocitiesConformToExpectations/VirtualSiteTest.WithinToleranceOfReference/35 (0 ms) 89: [----------] 36 tests from VelocitiesConformToExpectations/VirtualSiteTest (6266 ms total) 89: 89: [----------] Global test environment tear-down 89: [==========] 37 tests from 2 test suites ran. (6348 ms total) 89: [ PASSED ] 37 tests. 89/91 Test #89: MdrunVirtualSiteTests ........................ Passed 6.81 sec test 90 Start 90: EnsembleHistogramPotentialPlugin.ForceCalc 90: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxapi_extension_histogram-test "--gtest_filter=EnsembleHistogramPotentialPlugin.ForceCalc" 90: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests 90: Test timeout computed to be: 1500 90: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 90: Note: Google Test filter = EnsembleHistogramPotentialPlugin.ForceCalc 90: [==========] Running 1 test from 1 test suite. 90: [----------] Global test environment set-up. 90: [----------] 1 test from EnsembleHistogramPotentialPlugin 90: [ RUN ] EnsembleHistogramPotentialPlugin.ForceCalc 90: [ OK ] EnsembleHistogramPotentialPlugin.ForceCalc (0 ms) 90: [----------] 1 test from EnsembleHistogramPotentialPlugin (0 ms total) 90: 90: [----------] Global test environment tear-down 90: [==========] 1 test from 1 test suite ran. (0 ms total) 90: [ PASSED ] 1 test. 90/91 Test #90: EnsembleHistogramPotentialPlugin.ForceCalc ... Passed 0.08 sec test 91 Start 91: EnsembleBoundingPotentialPlugin.ForceCalc 91: Test command: /build/reproducible-path/gromacs-2024.4/build/mpi/bin/gmxapi_extension_bounding-test "--gtest_filter=EnsembleBoundingPotentialPlugin.ForceCalc" 91: Working Directory: /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/tests 91: Test timeout computed to be: 1500 91: Running main() from ./src/external/googletest/googletest/src/gtest_main.cc 91: Note: Google Test filter = EnsembleBoundingPotentialPlugin.ForceCalc 91: [==========] Running 1 test from 1 test suite. 91: [----------] Global test environment set-up. 91: [----------] 1 test from EnsembleBoundingPotentialPlugin 91: [ RUN ] EnsembleBoundingPotentialPlugin.ForceCalc 91: [ OK ] EnsembleBoundingPotentialPlugin.ForceCalc (0 ms) 91: [----------] 1 test from EnsembleBoundingPotentialPlugin (0 ms total) 91: 91: [----------] Global test environment tear-down 91: [==========] 1 test from 1 test suite ran. (0 ms total) 91: [ PASSED ] 1 test. 91/91 Test #91: EnsembleBoundingPotentialPlugin.ForceCalc .... Passed 0.07 sec 100% tests passed, 0 tests failed out of 91 Label Time Summary: GTest = 2943.04 sec*proc (87 tests) IntegrationTest = 2630.38 sec*proc (30 tests) MpiTest = 2227.65 sec*proc (23 tests) QuickGpuTest = 255.48 sec*proc (20 tests) SlowGpuTest = 2558.81 sec*proc (14 tests) SlowTest = 280.15 sec*proc (13 tests) UnitTest = 32.50 sec*proc (44 tests) Total Test time (real) = 1155.34 sec touch build-mpi dh_testdir (mkdir -p build/documentation ; cd build/documentation; \ LD_LIBRARY_PATH=/build/reproducible-path/gromacs-2024.4/build/documentation/lib cmake /build/reproducible-path/gromacs-2024.4 \ -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMXAPI=ON \ -DGMX_PYTHON_PACKAGE=ON -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON \ -DCMAKE_RULE_MESSAGES=OFF -DGMX_BUILD_MANUAL=ON -DGMX_BUILD_HELP=ON \ -DGMX_VERSION_STRING_OF_FORK="Debian-2024.4-1") -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3 (found suitable version "3.12.7", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - Success -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_PRAGMA -- Performing Test CXXFLAGS_PRAGMA - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - not supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway. If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on. -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: CXX -- Using default binary suffix: "" -- Using default library suffix: "" -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - not supported -- Detected build CPU vendor - ARM -- Detected build CPU brand - 0xd0c -- Detected build CPU family - 8 -- Detected build CPU model - 3 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - not present -- Checking for module 'fftw3f' -- Found fftw3f, version 3.3.10 -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_r2c in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_plan_many_dft_c2r in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_sse2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx2_128 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_avx_512 in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_kcvi in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_altivec in /usr/lib/aarch64-linux-gnu/libfftw3f.so - not found -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Looking for fftwf_have_simd_neon in /usr/lib/aarch64-linux-gnu/libfftw3f.so - found -- Using external FFT library - FFTW3 -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/aarch64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/aarch64-linux-gnu/liblapack.so;/usr/lib/aarch64-linux-gnu/libblas.so -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Failed CMake Deprecation Warning at src/external/googletest/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googlemock/CMakeLists.txt:39 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/external/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found Python: /usr/bin/python3 (found version "3.12.7") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION -- Performing Test HAVE_NO_DEBUG_DISABLES_OPTIMIZATION - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS -- Performing Test HAS_WARNING_NO_ARRAY_BOUNDS - Success -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE - Success -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Configuring Python package for gmxapi version 0.4.0 -- Using /build/reproducible-path/gromacs-2024.4/build/documentation/bin/gmx from build tree. -- Found pybind11: /usr/include (found version "2.13.6") -- Found Python interpreter: /usr/bin/python3 -- Python site-packages directory is /usr/lib/python./site-packages -- Found Doxygen: /usr/bin/doxygen (found version "1.9.8") found components: doxygen dot -- Found Sphinx: /usr/bin/sphinx-build (found suitable version "7.4.7", minimum required is "4.0.0") found components: pygments -- Found LATEX: /usr/bin/latex -- Configuring done (103.6s) -- Generating done (3.9s) -- Build files have been written to: /build/reproducible-path/gromacs-2024.4/build/documentation /usr/bin/make -j12 manual -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 manual make[2]: Entering directory 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/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -MD -MT src/gromacs/selection/CMakeFiles/scanner.dir/parser.cpp.o -MF CMakeFiles/scanner.dir/parser.cpp.o.d -o CMakeFiles/scanner.dir/parser.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/parser.cpp /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: 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/build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/lincs.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/lincs.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/event.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib/uncompr.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/huffmem.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/reduce_fast.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -Wno-deprecated-non-prototype -MD -MT src/gromacs/CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -MF CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o.d -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib/zutil.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/gather.cpp cd 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/scatter.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/group.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/tmpi_init.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/topology.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/rle.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/list.cpp [ 0%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/abstractoption.cpp.o -MF CMakeFiles/options.dir/abstractoption.cpp.o.d -o CMakeFiles/options.dir/abstractoption.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoption.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/tng_compress.c [ 1%] Built target tng_io_zlib /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/vals16.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/energyterm.cpp.o -MF CMakeFiles/energyanalysis.dir/energyterm.cpp.o.d -o CMakeFiles/energyanalysis.dir/energyterm.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/energyterm.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/warnmalloc.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/type.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserBase.cpp.o -MF CMakeFiles/muparser.dir/src/muParserBase.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserBase.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/muparser/src/muParserBase.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/widemuldiv.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/scan.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/numa_malloc.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc2.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -MF CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o.d -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/src/once.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/compression/xtc3.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o -MF CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/muparser/src/muParserBytecode.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/tng_io.c cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -I/build/reproducible-path/gromacs-2024.4/src/external/tng_io/external/zlib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-array-bounds -MD -MT src/gromacs/CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -MF CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o.d -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/reproducible-path/gromacs-2024.4/src/external/tng_io/src/lib/md5.c make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/maxwell.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/maxwell.png [ 3%] Built target thread_mpi /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/analysis/plots/sgangle.pdf /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/sgangle.pdf cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/docs/conf.cmakein.py -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/conf.py -D CMAKE_MINIMUM_REQUIRED_VERSION=3.18.4 -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=4.0.0 -D GMX_ADMIN_DIR=/build/reproducible-path/gromacs-2024.4/admin -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=This is not a release build of GROMACS, so please reference one of the GROMACS papers and the base release of the manual." -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D "GMX_SOURCE_DOI_STRING=This is not a release build of GROMACS. Please reference one of the GROMACS papers, as well as the base release that this version is built from. Also, please state what modifcations have been performed or where the version was sourced from." -D GMXAPI_PYTHON_STAGING_DIR=/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging -D IMAGE_CONVERT_STRING=gmx_image_convert_possible -D REGRESSIONTEST_VERSION=2024.4 -D REQUIRED_CUDA_COMPUTE_CAPABILITY=3.5 -D REQUIRED_CUDA_VERSION=11.0 -D REQUIRED_OPENCL_MIN_VERSION= -D REGRESSIONTEST_MD5SUM_STRING=unknown -D RELENG_PATH= -D SOURCE_MD5SUM=unknown -D SPHINX_EXTENSION_PATH=/build/reproducible-path/gromacs-2024.4/docs -D "GMX_CURRENT_CONTRIBUTORS_STRING=Mark Abraham, Andrey Alekseenko, Vladimir Basov, Cathrine Bergh, Eliane Briand, Ania Brown, Mahesh Doijade, Giacomo Fiorin, Stefan Fleischmann, Sergey Gorelov, Gilles Gouaillardet, Alan Gray, M. Eric Irrgang, Farzaneh Jalalypour, Joe Jordan, Carsten Kutzner, Justin A. Lemkul, Magnus Lundborg, Pascal Merz, Vedran Miletic, Dmitry Morozov, Julien Nabet, Szilard Pall, Andrea Pasquadibisceglie, Michele Pellegrino, Hubert Santuz, Roland Schulz, Tatiana Shugaeva, Alexey Shvetsov, Philip Turner, Alessandra Villa, Sebastian Wingbermuehle" -D "GMX_PREVIOUS_CONTRIBUTORS_STRING=Emile Apol, Rossen Apostolov, James Barnett, Paul Bauer, Herman J.C. Berendsen, Par Bjelkmar, Christian Blau, Viacheslav Bolnykh, Kevin Boyd, Aldert van Buuren, Carlo Camilloni, Rudi van Drunen, Anton Feenstra, Oliver Fleetwood, Vytas Gapsys, Gaurav Garg, Gerrit Groenhof, Bert de Groot, Anca Hamuraru, Vincent Hindriksen, Victor Holanda, Aleksei Iupinov, Christoph Junghans, Prashanth Kanduri, Dimitrios Karkoulis, Peter Kasson, Sebastian Kehl, Sebastian Keller, Jiri Kraus, Per Larsson, Viveca Lindahl, Erik Marklund, Pieter Meulenhoff, Teemu Murtola, Sander Pronk, Michael Shirts, Alfons Sijbers, Balint Soproni, David van der Spoel, Peter Tieleman, Carsten Uphoff, Jon Vincent, Teemu Virolainen, Christian Wennberg, Maarten Wolf, Artem Zhmurov" -D "GMX_CURRENT_PROJECT_LEADERS_STRING=Berk Hess, Erik Lindahl" -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/conf.py cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/mpmd-pme.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/mpmd-pme.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/c++ -DGMX_DOUBLE=0 -DMUPARSERLIB_EXPORTS -DMUPARSER_DLL -D_DEBUG -Dmuparser_EXPORTS -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -std=c++11 -fPIC -MD -MT _deps/muparser-build/CMakeFiles/muparser.dir/src/muParserCallback.cpp.o -MF CMakeFiles/muparser.dir/src/muParserCallback.cpp.o.d -o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/muparser/src/muParserCallback.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/texindex.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/texindex.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/download.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/download.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/links.dat /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/links.dat cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/api/gmxlibs.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/api/gmxlibs.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/nstric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/nstric.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/api/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/api/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/build-system.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/build-system.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/change-management.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/commitstyle.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/documentation-generation.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/par-lincs2.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/par-lincs2.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/contribute.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/contribute.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/doxygen.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/error-handling.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/formatting.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/formatting.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/gitlab-ci.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/gitlab-ci.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/gmxtree.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/gmxtree.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/includestyle.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/includestyle.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/pbctric.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/pbctric.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/infrastructure.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/infrastructure.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/known-issues.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/language-features.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/language-features.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/naming.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/naming.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/overview.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/overview.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/physical_validation.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/physical_validation.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/redmine-states.png /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/redmine-states.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/rhododec.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/rhododec.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/relocatable-binaries.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/relocatable-binaries.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/reportstyle.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/reportstyle.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/style.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/style.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/testutils.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/testutils.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/tools.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/tools.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/code-formatting.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/code-formatting.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/truncoct.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/truncoct.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/fragments/doxygen-links.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/fragments/doxygen-links.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/beginners.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/beginners.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/verlet-drift.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/algorithms/plots/verlet-drift.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/topology.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/topology.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/functions/plots/angle.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/functions/plots/angle.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/special.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/special.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/how-to/visualize.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/how-to/visualize.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/install-guide/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/install-guide/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/install-guide/exotic.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/install-guide/exotic.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/functions/plots/bstretch.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/functions/plots/bstretch.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/plots/GMX_logos/gmx_logo_blue.svg /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/plots/GMX_logos/gmx_logo_blue.svg cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert 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/build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2022/major/removed-functionality.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2022/major/removed-functionality.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/special/plots/gaussians.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2016/major/bugs-fixed.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2016/major/bugs-fixed.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2016/major/removed-features.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2016/major/removed-features.rst [ 3%] Built target linearalgebra /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/release-notes/2016/major/miscellaneous.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2016/major/miscellaneous.rst make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -MF CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o.d -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/mdrun.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/cmdline.rst 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&& /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/floating-point.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/user-guide/floating-point.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/flow.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/user-guide/flow.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/force-fields.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/user-guide/force-fields.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/getting-started.rst 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/build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/mdrun-performance.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/user-guide/mdrun-performance.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/run-time-errors.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/user-guide/run-time-errors.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/security.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/user-guide/security.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/system-preparation.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/user-guide/system-preparation.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/user-guide/terminology.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/user-guide/terminology.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/dev-manual/releng/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/dev-manual/releng/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/gmxapi/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/gmxapi/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy 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/build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/nblib/guide-to-writing-MD-programs.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/nblib/guide-to-writing-MD-programs.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/special/plots/pulldirrel.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/special/plots/pulldirrel.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/index.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/index.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/preface.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/preface.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/introduction.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/introduction.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/special/plots/pull.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/special/plots/pull.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/definitions.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/definitions.rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/topologies/topologies.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/topologies/topologies.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/special/plots/pullref.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/special/plots/pullref.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/topologies/particle-type.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst [ 3%] Built target scanner cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/topologies/parameter-files.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/topologies/parameter-files.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/topologies/molecule-definition.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/topologies/constraint-algorithm-section.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/topologies/constraint-algorithm-section.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/special/plots/rotation.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/special/plots/rotation.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/topologies/pdb2gmx-input-files.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/topologies/topology-file-formats.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/topologies/force-field-organization.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/topologies/force-field-organization.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/file-formats.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/file-formats.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/run-parameters.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/run-parameters.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/gm convert /build/reproducible-path/gromacs-2024.4/docs/reference-manual/analysis/plots/dih-def.pdf -antialias -quality 03 -pointsize 12 -density 1200 -units PixelsPerInch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input//reference-manual/analysis/plots/dih-def.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/details.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/details.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/averages.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/averages.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/references.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/references.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/plots/GMX_logos/gmx_falcon_blue.png /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/plots/GMX_logos/gmx_falcon_blue.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/plots/plotje.png /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/plots/plotje.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/plots/xvgr.png /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/plots/xvgr.png cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/algorithms.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/algorithms/algorithms.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy 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&& /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/simulated-annealing.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/algorithms/simulated-annealing.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/stochastic-dynamics.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/algorithms/stochastic-dynamics.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/brownian-dynamics.rst /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/algorithms/brownian-dynamics.rst cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy 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-I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/options.cpp.o -MF CMakeFiles/options.dir/options.cpp.o.d -o CMakeFiles/options.dir/options.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/algorithms/plots/free1.pdf /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/algorithms/plots/free1.pdf cd 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/build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdfO-O.pdf cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/docs/reference-manual/analysis/plots/rdf.pdf /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/reference-manual/analysis/plots/rdf.pdf cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include 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-g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/optionsvisitor.cpp.o -MF CMakeFiles/options.dir/optionsvisitor.cpp.o.d -o CMakeFiles/options.dir/optionsvisitor.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionsvisitor.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/options/CMakeFiles/options.dir/timeunitmanager.cpp.o -MF CMakeFiles/options.dir/timeunitmanager.cpp.o.d -o CMakeFiles/options.dir/timeunitmanager.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/options/timeunitmanager.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 35%] Built target tng_io_obj cd 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarbias_alb.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarbias_alb.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 35%] Built target mdrun_objlib cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong 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/build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_alchlambda.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_angles.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_angles.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_combination.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_combination.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_coordnums.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_coordnums.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/muparser.dir/link.txt --verbose=1 cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarcomp_distances.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvarcomp_distances.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-long-long -pedantic -g -Wl,--dependency-file,CMakeFiles/muparser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libmuparser.so.2 -o ../../lib/libmuparser.so.2.3.4 CMakeFiles/muparser.dir/src/muParser.cpp.o CMakeFiles/muparser.dir/src/muParserBase.cpp.o CMakeFiles/muparser.dir/src/muParserBytecode.cpp.o CMakeFiles/muparser.dir/src/muParserCallback.cpp.o CMakeFiles/muparser.dir/src/muParserDLL.cpp.o CMakeFiles/muparser.dir/src/muParserError.cpp.o CMakeFiles/muparser.dir/src/muParserInt.cpp.o CMakeFiles/muparser.dir/src/muParserTest.cpp.o CMakeFiles/muparser.dir/src/muParserTokenReader.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" cd /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build && /usr/bin/cmake -E cmake_symlink_library ../../lib/libmuparser.so.2.3.4 ../../lib/libmuparser.so.2 ../../lib/libmuparser.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 35%] Built target muparser /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/output.cpp.o -MF CMakeFiles/pulling.dir/output.cpp.o.d -o CMakeFiles/pulling.dir/output.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/output.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT 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-DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -MF CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o.d -o CMakeFiles/colvars_objlib.dir/__/external/colvars/colvartypes.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/external/colvars/colvartypes.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvarvalue.cpp.o -MF 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pull_rotation.cpp.o -MF CMakeFiles/pulling.dir/pull_rotation.cpp.o.d -o CMakeFiles/pulling.dir/pull_rotation.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pull_rotation.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o -MF CMakeFiles/pulling.dir/pullcoordexpressionparser.cpp.o.d -o 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/pulling/CMakeFiles/pulling.dir/pullutil.cpp.o -MF CMakeFiles/pulling.dir/pullutil.cpp.o.d -o CMakeFiles/pulling.dir/pullutil.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/pullutil.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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/build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -MF CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/compositesimulatorelement.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build cd 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src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -MF CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o.d -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/computeglobalselement.cpp make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src 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CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o.d -o CMakeFiles/taskassignment.dir/decidegpuusage.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -MF CMakeFiles/modularsimulator.dir/constraintelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/constraintelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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-c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/findallgputasks.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -MF CMakeFiles/modularsimulator.dir/domdechelper.cpp.o.d -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/domdechelper.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/energydata.cpp.o -MF CMakeFiles/modularsimulator.dir/energydata.cpp.o.d -o CMakeFiles/modularsimulator.dir/energydata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/energydata.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -MF CMakeFiles/taskassignment.dir/resourcedivision.cpp.o.d -o CMakeFiles/taskassignment.dir/resourcedivision.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/taskassignment.cpp.o -MF CMakeFiles/taskassignment.dir/taskassignment.cpp.o.d -o CMakeFiles/taskassignment.dir/taskassignment.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/taskassignment.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -MF CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o.d -o CMakeFiles/modularsimulator.dir/expandedensembleelement.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/expandedensembleelement.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/usergpuids.cpp.o -MF CMakeFiles/taskassignment.dir/usergpuids.cpp.o.d -o CMakeFiles/taskassignment.dir/usergpuids.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/usergpuids.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -MF CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o.d -o CMakeFiles/modularsimulator.dir/velocityscalingtemperaturecoupling.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/velocityscalingtemperaturecoupling.cpp make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 40%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation 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src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -MF 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -MF 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -MF 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ 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/build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -MF 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -MF 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/pulling/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/essentialdynamics/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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-DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include 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/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/atomdata.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src 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/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -MF CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o.d -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp cd 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_covar.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include 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/build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_current.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/correlationfunctions/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/fft/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/imd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mdspan/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/mimic/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/options/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/random/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/selection/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/statistics/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/swap/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tables/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/tools/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectory/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_density.cpp /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:42: In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp: In function 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)': /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:24: warning: '%s' directive writing up to 4095 bytes into a region of size 4094 [-Wformat-overflow=] 841 | sprintf(c, "%%d%s", str2); /* append '%s' and extention to filename */ | ^~ ~~~~ In function 'int sprintf(char*, const char*, ...)', inlined from 'void project(const char*, const t_topology*, PbcType, real (*)[3], const char*, const char*, const char*, const char*, const char*, int, const char*, gmx_bool, real, int, const t_atoms*, int, int*, gmx_bool, real (*)[3], int, int*, real*, const real*, real (*)[3], int*, real (**)[3], int, int*, gmx_bool, const gmx_output_env_t*)' at /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_anaeig.cpp:841:16: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 4098 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS 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/build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densmap.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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-isystem /build/reproducible-path/gromacs-2024.4/src/external/tng_io/include -isystem /build/reproducible-path/gromacs-2024.4/build/documentation/tng/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/muparser/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/lmfit -isystem /build/reproducible-path/gromacs-2024.4/src/external/colvars -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -MF CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_densorder.cpp At global scope: cc1plus: note: unrecognized command-line option '-Wno-cast-function-type-strict' may have been intended to silence earlier diagnostics cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/compat/include 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-MF CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o.d -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_dielectric.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/analysisdata/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/commandline/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -Wno-cast-function-type-strict -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -MF CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o.d -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/scattering.cpp.o -c /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include 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/usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lm /usr/lib/aarch64-linux-gnu/liblapack.so -lm ../../lib/libmuparser.so.2.3.4 cd /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.9.0.0 ../../lib/libgromacs.so.9 ../../lib/libgromacs.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 98%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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-I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas -Wno-missing-field-initializers -MD -MT api/gmxapi/CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -MF CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o.d -o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o -c /build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp/workflow.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/cpp -I/build/reproducible-path/gromacs-2024.4/src/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/src/include -I/build/reproducible-path/gromacs-2024.4/src -I/build/reproducible-path/gromacs-2024.4/src/gromacs/math/include -I/build/reproducible-path/gromacs-2024.4/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/legacy/include -I/build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include -isystem /build/reproducible-path/gromacs-2024.4/src/external/thread_mpi/include -isystem /build/reproducible-path/gromacs-2024.4/src/external -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fno-inline -Wno-unknown-pragmas 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/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,--dependency-file,CMakeFiles/gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../lib/libgmxapi.so.0.4.0 CMakeFiles/gmxapi.dir/cpp/resourceassignment.cpp.o CMakeFiles/gmxapi.dir/cpp/context.cpp.o CMakeFiles/gmxapi.dir/cpp/exceptions.cpp.o CMakeFiles/gmxapi.dir/cpp/gmxapi.cpp.o CMakeFiles/gmxapi.dir/cpp/md.cpp.o CMakeFiles/gmxapi.dir/cpp/mdmodule.cpp.o CMakeFiles/gmxapi.dir/cpp/mdsignals.cpp.o CMakeFiles/gmxapi.dir/cpp/session.cpp.o CMakeFiles/gmxapi.dir/cpp/status.cpp.o CMakeFiles/gmxapi.dir/cpp/system.cpp.o CMakeFiles/gmxapi.dir/cpp/version.cpp.o CMakeFiles/gmxapi.dir/cpp/workflow.cpp.o CMakeFiles/gmxapi.dir/cpp/tpr.cpp.o -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.9.0.0 -lm -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/documentation/lib cd /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgmxapi.so.0.4.0 ../../lib/libgmxapi.so.0 ../../lib/libgmxapi.so make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include 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-I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pycontext.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pysystem.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/wrapped_exceptions_0_3_1.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/mpi_bindings.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/pycontext_create.cpp cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/c++ -DGMX_DOUBLE=0 -D_gmxapi_EXPORTS -I/build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp -I/build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/src/cpp -I/usr/lib/python3/dist-packages/mpi4py/include -I/build/reproducible-path/gromacs-2024.4/api/gmxapi/include -I/build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/include -isystem /usr/include/python3.12 -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++17 -fPIC -fvisibility=hidden -MD -MT python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/src/cpp/mpi_no_gromacs_support.cpp.o -MF CMakeFiles/_gmxapi.dir/src/cpp/mpi_no_gromacs_support.cpp.o.d -o CMakeFiles/_gmxapi.dir/src/cpp/mpi_no_gromacs_support.cpp.o -c /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/mpi_no_gromacs_support.cpp /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp: In lambda function: /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:131:26: warning: 'void pybind11::exception::operator()(const char*) const [with type = gmxpy::Exception]' is deprecated: Please use py::set_error() instead (https://github.com/pybind/pybind11/pull/4772) [-Wdeprecated-declarations] 131 | baseException(message.c_str()); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.h:51, from /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:49: /usr/include/pybind11/pybind11.h:2625:10: note: declared here 2625 | void operator()(const char *message) const { set_error(*this, message); } | ^~~~~~~~ /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi/src/cpp/gmxpy_exceptions.cpp:137:29: warning: 'void pybind11::exception::operator()(const char*) const [with type = gmxpy::detail::export_exceptions(pybind11::module&)::UnknownExceptionPlaceHolder]' is deprecated: Please use py::set_error() instead (https://github.com/pybind/pybind11/pull/4772) [-Wdeprecated-declarations] 137 | unknownException(message.c_str()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/pybind11/pybind11.h:2625:10: note: declared here 2625 | void operator()(const char *message) const { set_error(*this, message); } | ^~~~~~~~ cd /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi && /usr/bin/cmake -E cmake_link_script CMakeFiles/_gmxapi.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gromacs-2024.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -Wl,--dependency-file,CMakeFiles/_gmxapi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o gmxapi_staging/gmxapi/_gmxapi.cpython-312-aarch64-linux-gnu.so CMakeFiles/_gmxapi.dir/src/cpp/launch_0_2_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/module.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_context.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_system.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/export_tprfile.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/gmxpy_exceptions.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pysystem.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/wrapped_exceptions_0_3_1.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_bindings.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/pycontext_create.cpp.o CMakeFiles/_gmxapi.dir/src/cpp/mpi_no_gromacs_support.cpp.o -Wl,-rpath,/build/reproducible-path/gromacs-2024.4/build/documentation/lib:/usr/lib/aarch64-linux-gnu/openmpi/lib ../../lib/libgmxapi.so.0.4.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so -Wl,-rpath-link,/build/reproducible-path/gromacs-2024.4/build/documentation/lib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target _gmxapi /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs 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/build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input && /usr/bin/cmake -E make_directory onlinehelp cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input && /build/reproducible-path/gromacs-2024.4/build/documentation/bin/gmx -quiet help -export rst make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f 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Try `pip install python-gitlab`. warnings.warn( /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst:131: WARNING: 'any' reference target not found: os.environ /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/commandline.py:docstring of gmxapi.commandline.commandline_operation:60: WARNING: 'any' reference target not found: os.getenv /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: sys.stderr /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging.basicConfig /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:13: WARNING: 'any' reference target not found: logging.StreamHandler /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2022/2022.1.rst:181: WARNING: 'any' reference target not found: subprocess.run cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual && /usr/bin/cmake -E chdir /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual /usr/bin/pdflatex -interaction=nonstopmode gromacs.tex This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./gromacs.tex LaTeX2e <2024-11-01> L3 programming layer <2024-11-02> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2024/06/29 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.MDSes sion' on page 611 undefined on input line 63415. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 611 undefined on input line 63436. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 611 undefined on input line 63436. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .TprFile' on page 611 undefined on input line 63501. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.TprFi le' on page 611 undefined on input line 63501. LaTeX Warning: Hyper reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi .SimulationParameters' on page 611 undefined on input line 63501. LaTeX Warning: Reference `gmxapi/userguide/pythonreference:gmxapi._gmxapi.Simul ationParameters' on page 611 undefined on input line 63501. [611] [612] Chapter 7. [613] [614] [615] [616] [617] Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Ker-nel SIMD type (\T1/pcr/m/n/10 SimdAuto\T1/ptm/m/n/10 /\T1/ pcr/m/n/10 SimdNo\T1/ptm/m/n/10 /\T1/pcr/m/n/10 Simd4XM\T1/ptm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 useHalfLJOptimizat Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 computeVirialAndEn Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Coulomb in-ter-ac-tion func-tion Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/pcr/m/n/10 useTabulatedEwaldC Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool Underfull \hbox (badness 10000) in paragraph at lines 64070--64070 []\T1/ptm/m/n/10 Bool [618] [619] Chapter 8. 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[519] [520 <./field.pdf>] [521] [522 <./compelsetup.pdf>] [523] [524] [525 <./dumtypes.pdf>] [526 <./dumaro.pdf>] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548 <./rdf.pdf> <./rdfO-O.pdf pdfTeX warning: /usr/bin/pdflatex (file ./rdfO-O.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [549] [550] [551] [552] [553 <./msdwater.pdf> <./dih-def.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dih-def.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [554 <./sgangle.pdf>] [555 <./distm.pdf>] [556] [557] [558 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] [559 <./phipsi.pdf>] [560 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] [561] [562] [563 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 9}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.57673 \sphinxAtStartPar ] [564] [565] [566 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 2}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.57969 \end{equation} ] [567] [568 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58122 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58122 \end{equation} ] [569 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage ] [570] [571] [572] [573] [574] [575] [576] [577] [578] Chapter 6. [579] [580] [581] [582] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60279. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60279. [583] [584] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60466. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60466. Overfull \vbox (1.84944pt too high) detected at line 60523 [585] [586] Underfull \hbox (badness 10000) in paragraph at lines 60665--60668 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [587] [588] [589] [590] [591] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61110. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61110. [592] [593] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61275. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61275. 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[621] [622] [623] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [624] [625 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [626] [627] [628] [629] [630] [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 66702--66708 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 6575) in paragraph at lines 67784--67790 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. 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[519] [520 <./field.pdf>] [521] [522 <./compelsetup.pdf>] [523] [524] [525 <./dumtypes.pdf>] [526 <./dumaro.pdf>] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548 <./rdf.pdf> <./rdfO-O.pdf pdfTeX warning: /usr/bin/pdflatex (file ./rdfO-O.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [549] [550] [551] [552] [553 <./msdwater.pdf> <./dih-def.pdf pdfTeX warning: /usr/bin/pdflatex (file ./dih-def.pdf): PDF inclusion: multiple pdfs with page group included in a single page >] [554 <./sgangle.pdf>] [555 <./distm.pdf>] [556] [557] [558 <./hbond.pdf> <./hbond-insert.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hbond-insert.pdf): PDF inclusion: mul tiple pdfs with page group included in a single page >] [559 <./phipsi.pdf>] [560 <./rama.pdf> <./hpr-wheel.pdf pdfTeX warning: /usr/bin/pdflatex (file ./hpr-wheel.pdf): PDF inclusion: multip le pdfs with page group included in a single page >] [561] [562] [563 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.44 9}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.57673 \sphinxAtStartPar ] [564] [565] [566 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.46 2}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.57969 \end{equation} ] [567] [568 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58122 \end{equation} pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 4}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58122 \end{equation} ] [569 pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage pdfTeX warning (ext4): destination with the same identifier (name{equation.5.47 8}) has been already used, duplicate ignored ...shipout:D \box_use:N \l_shipout_box \__shipout_drop_firstpage_... l.58167 \clearpage ] [570] [571] [572] [573] [574] [575] [576] [577] [578] Chapter 6. [579] [580] [581] [582] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60279. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60279. [583] [584] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60466. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 60466. Overfull \vbox (1.84944pt too high) detected at line 60523 [585] [586] Underfull \hbox (badness 10000) in paragraph at lines 60665--60668 []\T1/ptm/m/n/10 The fol-low-ing in-struc-tions are para-phrased from [][]$http s : / / pip . pypa . io / en / stable / user _ guide / [587] [588] [589] [590] [591] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61110. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61110. [592] [593] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61275. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 61275. 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[621] [622] [623] pdfTeX warning: /usr/bin/pdflatex (file ./graphviz-d18d8687359a04d68afb2d653619 8981190fe142.pdf): PDF inclusion: found PDF version <1.7>, but at most version <1.5> allowed [624] [625 <./graphviz-d18d8687359a04d68afb2d6536198981190fe142.pdf>] [626] [627] [628] [629] [630] [631] [632] [633] [634] [635] [636] [637] [638] [639] [640] [641] [642] Underfull \hbox (badness 10000) in paragraph at lines 66702--66708 []\T1/ptm/m/n/10 The above logic to find the in-stal-la-tion pre-fix is in \T1/ pcr/m/n/10 src/gromacs/commandline/ [643] [644] [645] [646] [647] [648] [649] [650] [651] [652] Underfull \hbox (badness 6575) in paragraph at lines 67784--67790 []\T1/ptm/m/n/10 Use smart point-ers for mem-ory man-age-ment. By de-fault, use \T1/pcr/m/n/10 std::unique_-ptr \T1/ptm/m/n/10 and [653] [654] [655 <./redmine-states.png>] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] Underfull \vbox (badness 1590) detected at line 69174 [667] Underfull \vbox (badness 10000) detected at line 69174 Underfull \vbox (badness 10000) detected at line 69174 [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 70418. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 70418. Package textcomp Warning: Symbol \textasciigrave not provided by (textcomp) font family pcr in TS1 encoding. (textcomp) Default family used instead on input line 70418. 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Underfull \hbox (badness 10000) in paragraph at lines 72302--72306 \T1/ptm/m/n/10 (page 702[]) can be found at \T1/pcr/m/n/10 $GROMACS_-ROOT/share /cmake/gromacs$GROMACS_-SUFFIX/ [700] [701] [702] Underfull \hbox (badness 7344) in paragraph at lines 72652--72656 []\T1/ptm/m/n/10 CMake tar-get \T1/pcr/m/n/10 Gromacs::libgromacs\T1/ptm/m/n/10 , en-abled by [][]\T1/pcr/m/sl/10 GMX_-INSTALL_-LEGACY_-API[][] [703] Chapter 11. [704] [705] [706] [707] [708] [709] [710] [711] Underfull \hbox (badness 7168) in paragraph at lines 73283--73288 []\T1/ptm/m/n/10 In some cases, GRO-MACS could ran-domly crash on neighbor-sear ch steps with \T1/pcr/m/n/10 hip_-queue: [712] [713] Underfull \hbox (badness 10000) in paragraph at lines 73441--73445 []\T1/pcr/m/n/10 NbnxmSetupTest.CanCreateNbnxmGPU \T1/ptm/m/n/10 could crash in GPU builds with an er-ror in [714] [715] [716] [717] [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] Underfull \hbox (badness 7722) in paragraph at lines 74751--74756 []\T1/ptm/m/n/10 De-pend-ing on the build en-vi-ron-ment, GRO-MACS 2023 and 202 3.1 could in-stall a mal-formed [731] [732] [733] [734] [735] [736] [737] [738] [739] [740] [741] [742] [743] [744] [745] [746] [747] [748] [749] [750] [751] [752] [753] [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776] [777] [778] [779] [780] [781] [782] [783] [784] [785] [786] [787] [788] [789] [790] [791] [792] [793] [794] [795] [796] [797] [798] [799] [800] [801] [802] [803] [804] [805] [806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817] [818] [819] [820] [821] [822] [823] [824] [825] [826] [827] [828] [829] [830] [831] [832] [833] [834] [835] [836] [837] [838] [839] [840] [841] [842] [843] [844] [845] [846] [847] [848] [849] [850] [851] [852] [853] [854] [855] [856] [857] [858] [859] [860] [861] [862] [863] [864] [865] [866] [867] [868] [869] [870] [871] [872] [873] [874] [875] Overfull \hbox (18.01631pt too wide) in paragraph at lines 85908--85911 []\T1/ptm/m/n/10 Changed multi-simulation nsteps be-haviour ^^P^^Q^^Q^^Q^^Q^^Q^ ^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^ Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q^^Q ^^Q^^Q^^Q^^Q^^Q^^Q^^Q- Underfull \hbox (badness 10000) in paragraph at lines 85908--85911 [876] [877] [878] [879] [880] [881] [882] [883] [884] [885] [886] [887] [888] [889] [890] [891] No file gromacs.ind. 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'/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation 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/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build [ 4%] Built target sphinx-image-conversion make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 4%] Built target scanner make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend [ 4%] Built target release-version-info [ 6%] Built target tng_io_obj make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs 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Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/external/muparser /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build /build/reproducible-path/gromacs-2024.4/build/documentation/_deps/muparser-build/CMakeFiles/muparser.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && 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/build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for '_deps/muparser-build/CMakeFiles/muparser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 9%] Built target linearalgebra [ 9%] Built target lmfit_objlib [ 9%] Built target energyanalysis [ 9%] Built target muparser [ 9%] Built target options /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend [ 35%] Built target sphinx-input-rst [ 38%] Built target colvars_objlib [ 38%] Built target gmx_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target mdrun_objlib make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 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'/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 40%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs 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'/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make 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Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target sphinx-input /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs 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/build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/man.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/man.dir/build.make docs/CMakeFiles/man.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/sphinx-build -q -b man -w sphinx-man.log -d /build/reproducible-path/gromacs-2024.4/build/documentation/docs/_man_doctrees -t do_man /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2024.4/build/documentation/docs/man WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2024.4/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target man make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -j12 webpage -C build/documentation make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 webpage make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles 65 /usr/bin/make -f CMakeFiles/Makefile2 docs/CMakeFiles/webpage.dir/all make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs 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'/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build /usr/bin/make -f _deps/muparser-build/CMakeFiles/muparser.dir/build.make _deps/muparser-build/CMakeFiles/muparser.dir/build [ 0%] Built target release-version-info make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for '_deps/muparser-build/CMakeFiles/muparser.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 4%] Built target sphinx-image-conversion [ 4%] Built target scanner [ 6%] Built target thread_mpi [ 7%] Built target tng_io_zlib [ 9%] Built target tng_io_obj [ 12%] Built target colvars_objlib /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend [ 12%] Built target lmfit_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" [ 12%] Built target muparser /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend [ 12%] Built target linearalgebra make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-input-rst.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 12%] Built target options [ 12%] Built target energyanalysis /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/depend [ 38%] Built target sphinx-input-rst [ 38%] Built target mdrun_objlib /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-version.dir/DependInfo.cmake "--color=" [ 38%] Built target gmx_objlib make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-source-timestamp.txt /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -D VERSION_VARIABLES=/build/reproducible-path/gromacs-2024.4/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/docs/doxygen/Doxyfile-version.cmakein -D VERSION_OUT=Doxyfile-version -P /build/reproducible-path/gromacs-2024.4/cmake/gmxConfigureVersionInfo.cmake [ 38%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend [ 38%] Built target doxygen-source-timestamp /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 38%] Built target taskassignment make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 38%] Built target doxygen-version /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 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The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs /build/reproducible-path/gromacs-2024.4/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 98%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs /build/reproducible-path/gromacs-2024.4/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [ 98%] Built target gmx [100%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi 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/build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/CMakeFiles/sphinx-programs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target sphinx-programs /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/manual /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual/CMakeFiles/pdf.dir/DependInfo.cmake "--color=" warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 15 of file 'Doxyfile-xml' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/pdf.dir/build.make docs/manual/CMakeFiles/pdf.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/pdf.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target pdf /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/manual /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual/CMakeFiles/manual.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/manual/CMakeFiles/manual.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target manual /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/webpage-sphinx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/sphinx-build -q -b html -w sphinx-html.log -d /build/reproducible-path/gromacs-2024.4/build/documentation/docs/_html_doctrees -t do_html /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input /build/reproducible-path/gromacs-2024.4/build/documentation/docs/html WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by NameResolutionError(": Failed to resolve 'docs.python.org' ([Errno -3] Temporary failure in name resolution)")) WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://mpi4py.readthedocs.io/en/stable/objects.inv' not fetchable due to : HTTPSConnectionPool(host='mpi4py.readthedocs.io', port=443): Max retries exceeded with url: /en/stable/objects.inv (Caused by NameResolutionError(": Failed to resolve 'mpi4py.readthedocs.io' ([Errno -3] Temporary failure in name resolution)")) /build/reproducible-path/gromacs-2024.4/admin/trigger-post-merge.py:53: UserWarning: This tool requires the `gitlab` package. Try `pip install python-gitlab`. warnings.warn( The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp:44: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule.cpp:49: warning: no matching class member found for gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintForceProvider::RestraintForceProvider()=delete' at line 212 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 223 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule.cpp:153: warning: no matching class member found for gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites) Possible candidates: 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl()=delete' at line 271 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(std::shared_ptr< gmx::IRestraintPotential > restraint, const std::vector< int > &sites)' at line 278 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h 'gmx::RestraintMDModuleImpl::RestraintMDModuleImpl(RestraintMDModuleImpl &&) noexcept=default' at line 286 of file /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/arrayref.h:314: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:268: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:247: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:247: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:268: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:175: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:247: warning: @copybrief or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:248: warning: @copydetails or @copydoc target 'CheckpointData::scalar' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:255: warning: @copybrief or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:255: warning: @copydetails or @copydoc target 'CheckpointData::arrayRef' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:265: warning: @copybrief or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:265: warning: @copydetails or @copydoc target 'CheckpointData::tensor' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:268: warning: @copybrief or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:269: warning: @copydetails or @copydoc target 'CheckpointData::subCheckpointData' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:159: warning: @copydetails or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:310: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:357: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:359: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:93: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:98: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:119: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:124: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/topology/index.h:102: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/topology/index.h:99: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:153: warning: @copybrief or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:154: warning: @copydetails or @copydoc target 'warning_error_and_exit(WarningHandler*,const char *,int,const char *,int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/topology/index.h:102: warning: Illegal command @param found as part of a \p command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/topology/index.h:99: warning: The following parameter of write_index(const char *outf, gmx::ArrayRef< const IndexGroup > indexGroups, bool duplicate, int numAtoms) is not documented: parameter 'numAtoms' /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-xml-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-xml /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-user.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/dep-graphs-dot.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/python3 /build/reproducible-path/gromacs-2024.4/docs/doxygen/graphbuilder.py -S /build/reproducible-path/gromacs-2024.4 -B /build/reproducible-path/gromacs-2024.4/build/documentation -o /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" /build/reproducible-path/gromacs-2024.4/docs/doxygen/doxygenxml.py:35: SyntaxWarning: invalid escape sequence '\l' """Doxygen XML output parser. /build/reproducible-path/gromacs-2024.4/docs/doxygen/doxygenxml.py:349: SyntaxWarning: invalid escape sequence '\i' self, "\internal does not cover whole documentation" /build/reproducible-path/gromacs-2024.4/docs/doxygen/doxygenxml.py:356: SyntaxWarning: invalid escape sequence '\l' self, "\libinternal should not be used inside \internal" Scanning source tree... Reading source files... Reading Doxygen XML files... Writing graphs... cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/dep-graphs-dot-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target dep-graphs-dot /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-full.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/depgraphs cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... NOTE: You are using Doxygen version 1.9.8. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 40 of file 'Doxyfile-common' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp:44: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpwritercontext.cpp:246: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/testasserts.h:738: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/src/testutils/testasserts.cpp:182: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:57: warning: Member int64_to_int found in multiple @ingroup groups! The member will be put in group module_utility, and not in group group_libraryapi /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/basedefinitions.h:208: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/iframeconverter.h:109: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:57: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:78: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:94: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:108: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:130: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:167: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member __attribute__((always_inline)) static AmdPackedFloat3 operator*(const AmdPackedFloat3 &v (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member s (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:325: warning: Member v (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/int64_to_int.h:48: warning: Found unknown command '\file' /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((ext_vector_type(2))) Native_float2_ (typedef) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((packed)) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:240: warning: Member __attribute__((always_inline)) float operator[](Index i) const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:250: warning: Member __attribute__((always_inline)) float &operator[](Index i) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:260: warning: Member __attribute__((always_inline)) float x() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:261: warning: Member __attribute__((always_inline)) float y() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:262: warning: Member __attribute__((always_inline)) Native_float2_ xy() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:263: warning: Member __attribute__((always_inline)) float z() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:267: warning: Member AmdPackedFloat3(float x, float y, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:269: warning: Member AmdPackedFloat3(Native_float2_ xy, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:271: warning: Member AmdPackedFloat3(Float3 r) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:273: warning: Member operator Float3() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraint_gpu_helpers.h:51: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:66: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:67: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:68: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.h:241: warning: Member PackedJClusterList(const gmx::PinningPolicy pinningPolicy) (function) of class PackedJClusterList is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:70: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:67: warning: Member CheckpointDataOperation (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/referencetemperaturemanager.h:66: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:117: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:131: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:251: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/massrepartitioning.cpp:44: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:451: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:88: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:108: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:733: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:742: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:749: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:755: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:881: warning: Member getConnection(Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/simulatoralgorithm.h:608: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:2586: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:165: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:172: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:80: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp:55: warning: Member c_forces (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:118: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:108: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:110: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:115: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:116: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:121: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:122: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:126: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:129: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:130: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:131: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:133: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:134: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:98: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:93: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:124: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:119: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:108: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:163: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:440: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:137: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:332: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:483: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:179: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:209: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:231: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:270: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:144: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member swap(SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:125: warning: Member mode (typedef) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp:122: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp:135: warning: Member getGridOffset(gmx::ArrayRef< const Grid > grids, int gridIndex) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:63: warning: Member nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid &grid, NbnxmGpu *nb, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const gmx::AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:83: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:97: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:128: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:178: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:202: warning: Member initPlistSorting(gpuPlistSorting *sorting) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:225: warning: Member init_plist(gpu_plist *pl) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:253: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:302: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:356: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:442: warning: Member gpu_init(const gmx::DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:511: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:528: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:689: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:792: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:823: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:829: warning: Member setupGpuShortRangeWork(NbnxmGpu *nb, const gmx::ListedForcesGpu *listedForcesGpu, const gmx::InteractionLocality iLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:842: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const gmx::InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:981: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1076: warning: Member nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1286: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1292: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp:355: warning: Member getENbnxnInitCombRule(const t_forcerec &forcerec) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:106: warning: Member elecEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:109: warning: Member elecEwaldTab (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:112: warning: Member ljEwald (variable) of namespace Nbnxm is not documented. cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-user-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-user libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp:44: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2024.4/src/gromacs/onlinehelp/helpwritercontext.cpp:246: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/src/testutils/testasserts.cpp:182: warning: unbalanced grouping commands /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/basedefinitions.h:208: warning: documentation for unknown define GMX_IGNORE_RETURN_VALUE found. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.h:316: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (65), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (71), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_struct.h:113: warning: Member gmx_domdec_zone_size_t (typedef) of file domdec_struct.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.h:316: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.h:221: warning: unable to resolve reference to 'gmx_pme_reinit' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme.h:316: warning: unable to resolve reference to 'pme_gpu_supports_input' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/devicebuffer_ocl.h:386: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/devicebuffer_sycl.h:437: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:61: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:62: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:63: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:77: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:79: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:84: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:86: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:91: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:92: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:92: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gputraits.h:63: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:57: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:78: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:94: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:108: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:130: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:167: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member __attribute__((always_inline)) static AmdPackedFloat3 operator*(const AmdPackedFloat3 &v (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member s (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:325: warning: Member v (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:52: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:62: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:175: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:185: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:194: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:84: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:86: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:88: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:88: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:108: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:647: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:658: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:693: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:704: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:738: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:747: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:746: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:517: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:523: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:541: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:547: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:633: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:662: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:666: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:670: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:708: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:712: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:716: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:379: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:484: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include/gromacs/timing/gpu_timing.h:57: warning: Member PmeStage (enumeration) of file gpu_timing.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility.h:109: warning: explicit link request to 'GMX_IGNORE_RETURN_VALUE' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((ext_vector_type(2))) Native_float2_ (typedef) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((packed)) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:240: warning: Member __attribute__((always_inline)) float operator[](Index i) const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:250: warning: Member __attribute__((always_inline)) float &operator[](Index i) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:260: warning: Member __attribute__((always_inline)) float x() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:261: warning: Member __attribute__((always_inline)) float y() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:262: warning: Member __attribute__((always_inline)) Native_float2_ xy() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:263: warning: Member __attribute__((always_inline)) float z() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:267: warning: Member AmdPackedFloat3(float x, float y, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:269: warning: Member AmdPackedFloat3(Native_float2_ xy, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:271: warning: Member AmdPackedFloat3(Float3 r) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:273: warning: Member operator Float3() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraint_gpu_helpers.h:51: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:176: warning: Member supportedSubGroupSizes() const (function) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:175: warning: Member supportedSubGroupSizesSize (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:181: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:66: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:67: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:68: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:68: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:73: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:77: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm.h:482: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.h:241: warning: Member PackedJClusterList(const gmx::PinningPolicy pinningPolicy) (function) of class PackedJClusterList is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:70: warning: Member CacheLineAlignedFlag (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft.h:67: warning: Member FftBackend (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/referencetemperaturemanager.h:66: warning: Member ReferenceTemperatureChangeAlgorithm (enumeration) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:117: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:131: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:251: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/massrepartitioning.cpp:44: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:451: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:88: warning: Member makeCheckpointArrayRef(T &container) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:108: warning: Member makeCheckpointArrayRefFromArray(T *begin, size_t size) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:733: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:742: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:749: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:755: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:881: warning: Member getConnection(Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/simulatoralgorithm.h:608: warning: Member getElementPointer(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:2586: warning: Member compileSelection(SelectionCollection *coll) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:165: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:172: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/template_mp.h:87: warning: Member dispatchTemplatedFunction(Function &&f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:80: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp:55: warning: Member c_forces (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:118: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:108: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:110: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:115: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:116: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:121: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:122: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:126: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:129: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:130: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:131: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:133: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:134: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:379: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:746: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:517: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:523: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:541: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:547: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:633: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:662: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:666: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:670: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:708: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:712: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:716: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:310: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:357: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:359: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:98: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:93: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:124: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:119: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:157: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:158: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:159: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:108: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:163: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:253: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:275: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:230: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:236: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:241: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:261: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:269: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:182: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:440: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:106: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:107: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:108: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange.h:100: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange.h:101: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:137: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:143: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:148: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:153: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:158: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:159: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:161: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:162: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:163: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:164: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:167: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:169: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:332: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:483: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:179: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:209: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:231: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:270: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:85: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.h:145: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.h:391: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:89: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:90: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:91: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:144: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member swap(SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:341: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:343: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:348: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:353: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:367: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:394: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:399: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:404: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:159: warning: @copydetails or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:112: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:113: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:114: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:412: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/mp11.h:76: warning: Member mp_with_index(std::size_t i, F &&f) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:70: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/hbond.cpp:70: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.h:60: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:69: warning: Member SimulationRunnerMdpSource (enumeration) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:68: warning: Member awhDimParamSerialized(AwhCoordinateProviderType inputCoordinateProvider, int inputCoordIndex, double inputOrigin, double inputEnd, double inputPeriod, double inputDiffusion) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:110: warning: Member awhBiasParamSerialized(AwhHistogramGrowthType eawhgrowth, double beta, double inputErrorScaling, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int shareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.cpp:167: warning: Member awhParamSerialized(AwhHistogramGrowthType eawhgrowth, AwhPotentialType eawhpotential, double beta, double inputErrorScaling, int64_t inputSeed, ArrayRef< const std::vector< char > > dimensionParameterBuffers, int biasShareGroup, bool inputUserData, AwhTargetType eTargetType, bool scaleTargetByMetric) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp:66: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.cpp:398: warning: Member getNumberOfTestOpenMPThreads() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:61: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:74: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:87: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:108: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp:429: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:414: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:408: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:416: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:68: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:69: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:70: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:71: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:263: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:267: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:783: warning: Member testKernelTypes (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:125: warning: Member mode (typedef) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp:122: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp:135: warning: Member getGridOffset(gmx::ArrayRef< const Grid > grids, int gridIndex) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:63: warning: Member nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid &grid, NbnxmGpu *nb, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const gmx::AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:83: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:97: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:128: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:178: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:202: warning: Member initPlistSorting(gpuPlistSorting *sorting) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:225: warning: Member init_plist(gpu_plist *pl) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:253: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:302: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:356: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:442: warning: Member gpu_init(const gmx::DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:511: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:528: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:689: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:792: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:823: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:829: warning: Member setupGpuShortRangeWork(NbnxmGpu *nb, const gmx::ListedForcesGpu *listedForcesGpu, const gmx::InteractionLocality iLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:842: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const gmx::InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:981: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1076: warning: Member nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1286: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1292: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp:355: warning: Member getENbnxnInitCombRule(const t_forcerec &forcerec) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:106: warning: Member elecEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:109: warning: Member elecEwaldTab (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:112: warning: Member ljEwald (variable) of namespace Nbnxm is not documented. cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-lib-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-lib /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/commandline.py:docstring of gmxapi.commandline.commandline_operation:60: WARNING: 'any' reference target not found: os.getenv /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: sys.stderr /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:6: WARNING: 'any' reference target not found: logging.basicConfig /build/reproducible-path/gromacs-2024.4/build/documentation/python_packaging/gmxapi/gmxapi_staging/gmxapi/_logging.py:docstring of gmxapi._logging:13: WARNING: 'any' reference target not found: logging.StreamHandler /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/gmxapi/userguide/usage.rst:131: WARNING: 'any' reference target not found: os.environ /build/reproducible-path/gromacs-2024.4/build/documentation/docs/sphinx-input/release-notes/2022/2022.1.rst:181: WARNING: 'any' reference target not found: subprocess.run make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target webpage-sphinx The following warnings were produced by Doxygen: /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/biasgrid.h:279: warning: the \endcond does not have a corresponding \cond in this file /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/energyhistory.cpp:44: warning: Conditional section with label 'INTERNAL' does not have a corresponding \endcond command within this file. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/arrayref.h:314: warning: @copybrief or @copydoc target 'arrayRefFromArray' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'functions.h' not generated, too many nodes (56), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basicoptions.h' not generated, too many nodes (51), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved warning: Included by graph for 'arrayref.h' not generated, too many nodes (193), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes (124), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes (60), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'enumerationhelpers.h' not generated, too many nodes (56), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'exceptions.h' not generated, too many nodes (230), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes (228), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes (132), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'smalloc.h' not generated, too many nodes (98), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'stringutil.h' not generated, too many nodes (208), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxy_gromacs_version.h:42: warning: Member COLVARPROXY_VERSION (macro definition) of file colvarproxy_gromacs_version.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:80: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:87: warning: Member Ensures(cond) (macro definition) of file pointers.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/iframeconverter.h:116: warning: invalid argument for command '\iline' /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/computemultibodycutoffs.cpp:267: warning: Member dd_bonded_cg_distance(const gmx::MDLogger &mdlog, const gmx_mtop_t &mtop, const t_inputrec &inputrec, ArrayRef< const RVec > x, const matrix box, const DDBondedChecking ddBondedChecking, real *r_2b, real *r_mb) (function) of file computemultibodycutoffs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:140: warning: Member dd_sendrecv2_rvec(const struct gmx_domdec_t gmx_unused *dd, int gmx_unused ddimind, rvec gmx_unused *buf_s_fw, int gmx_unused n_s_fw, rvec gmx_unused *buf_r_fw, int gmx_unused n_r_fw, rvec gmx_unused *buf_s_bw, int gmx_unused n_s_bw, rvec gmx_unused *buf_r_bw, int gmx_unused n_r_bw) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:226: warning: Member dd_bcast(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, void gmx_unused *data) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:236: warning: Member dd_scatter(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:255: warning: Member dd_gather(const gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void gmx_unused *dest) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:274: warning: Member dd_scatterv(const gmx_domdec_t gmx_unused *dd, gmx::ArrayRef< const int > gmx_unused scounts, gmx::ArrayRef< const int > gmx_unused disps, const T *sbuf, int rcount, T *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:317: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const int *sbuf, int rcount, int *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:324: warning: Member dd_scatterv(const gmx_domdec_t *dd, gmx::ArrayRef< const int > scounts, gmx::ArrayRef< const int > disps, const gmx::RVec *sbuf, int rcount, gmx::RVec *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:332: warning: Member dd_gatherv(const gmx_domdec_t gmx_unused *dd, int gmx_unused scount, const T gmx_unused *sbuf, gmx::ArrayRef< const int > gmx_unused rcounts, gmx::ArrayRef< const int > gmx_unused disps, T gmx_unused *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:371: warning: Member dd_gatherv(const gmx_domdec_t *dd, int scount, const int *sbuf, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, int *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_network.cpp:378: warning: Member dd_gatherv(const gmx_domdec_t *dd, int scount, const gmx::RVec *sbuf, gmx::ArrayRef< const int > rcounts, gmx::ArrayRef< const int > disps, gmx::RVec *rbuf) (function) of file domdec_network.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/domdec_struct.h:113: warning: Member gmx_domdec_zone_size_t (typedef) of file domdec_struct.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:63: warning: Member supportedLibMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu.cpp:66: warning: Member supportedThreadMpiBuild (variable) of file gpuhaloexchange_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:117: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:131: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/localtopology.cpp:946: warning: Member dd_make_local_top(const gmx_domdec_t &dd, const gmx_domdec_zones_t &zones, int npbcdim, matrix box, rvec cellsize_min, const ivec npulse, t_forcerec *fr, ArrayRef< const RVec > coordinates, const gmx_mtop_t &mtop, gmx::ArrayRef< const int64_t > atomInfo, gmx_localtop_t *ltop) (function) of file localtopology.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/reversetopology.cpp:401: warning: Member dd_make_reverse_top(FILE *fplog, gmx_domdec_t *dd, const gmx_mtop_t &mtop, const gmx::VirtualSitesHandler *vsite, const t_inputrec &inputrec, const DDBondedChecking ddBondedChecking) (function) of file reversetopology.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/ewald.cpp:71: warning: Member cvec (typedef) of file ewald.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:57: warning: Member hardware_destructive_interference_size (variable) of file pme_force_sender_gpu_impl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gather_sycl.cpp:699: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gather_sycl.cpp:703: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gather_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu.cpp:281: warning: Member pme_gpu_launch_gather(const gmx_pme_t *pme, gmx_wallcycle gmx_unused *wcycle, const real lambdaQ, const bool computeVirial) (function) of file pme_gpu.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:90: warning: Member mode (typedef) of file pme_gpu_calculate_splines_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:49: warning: Member gmx_parallel_3dfft_t (typedef) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:105: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft_t *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:110: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft_t *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:115: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid.h:119: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, int) (function) of file pme_gpu_grid.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:61: warning: Member mode (typedef) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1403: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft_t *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1408: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, float *h_fftRealGrid, gmx_parallel_3dfft_t *fftSetup, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1413: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_grid_sycl.cpp:1417: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *pmeGpu, DeviceBuffer< float > *d_fftRealGrid, const int gridIndex) (function) of file pme_gpu_grid_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_internal.cpp:1120: warning: Member pme_gpu_update_input_box(PmeGpu gmx_unused *pmeGpu, const matrix gmx_unused box) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_internal.cpp:2525: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_internal.h:69: warning: Member gmx_parallel_3dfft_t (typedef) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_internal.h:450: warning: Member pme_gpu_set_kernelparam_useNvshmem(const PmeGpu *pmeGpu, bool useNvshmem) (function) of file pme_gpu_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:82: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, float *, gmx_parallel_3dfft_t *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:87: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, float *, gmx_parallel_3dfft_t *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:92: warning: Member convertPmeGridToFftGrid< true >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_ocl_stubs.cpp:96: warning: Member convertPmeGridToFftGrid< false >(const PmeGpu *, DeviceBuffer< float > *, const int) (function) of file pme_gpu_ocl_stubs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:91: warning: Member INSTANTIATE_SPREAD_2( order, computeSplines, spreadCharges, numGrids, writeGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:94: warning: Member INSTANTIATE_SPREAD(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:100: warning: Member INSTANTIATE_GATHER_2(order, numGrids, readGlobal, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:103: warning: Member INSTANTIATE_GATHER(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:107: warning: Member INSTANTIATE_X(x, order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:113: warning: Member INSTANTIATE_SOLVE(subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:123: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:59: warning: Member c_pmeOrder (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:61: warning: Member c_wrapX (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:62: warning: Member c_wrapY (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:64: warning: Member c_stateA (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl_sycl.cpp:65: warning: Member c_stateB (variable) of file pme_gpu_program_impl_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_types_host.h:72: warning: Member PmeGpuHaloExchange (typedef) of file pme_gpu_types_host.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_internal.h:79: warning: Member PME_GRID_C6A (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_internal.h:85: warning: Member DO_Q_AND_LJ (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_internal.h:86: warning: Member DO_Q_AND_LJ_LB (macro definition) of file pme_internal.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp.cpp:477: warning: Member gmx_pme_send_resetcounters(const t_commrec gmx_unused *cr, int64_t gmx_unused step) (function) of file pme_pp.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:76: warning: Member PP_PME_CHARGEB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:77: warning: Member PP_PME_SQRTC6 (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:78: warning: Member PP_PME_SQRTC6B (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:79: warning: Member PP_PME_SIGMA (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:80: warning: Member PP_PME_SIGMAB (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:81: warning: Member PP_PME_COORD (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:82: warning: Member PP_PME_ENER_VIR (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:83: warning: Member PP_PME_FINISH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:84: warning: Member PP_PME_SWITCHGRID (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:85: warning: Member PP_PME_RESETCOUNTERS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:86: warning: Member PP_PME_GPUCOMMS (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:88: warning: Member PP_PME_RECVFTOGPU (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:90: warning: Member PP_PME_MDGPUGRAPH (macro definition) of file pme_pp_communication.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_solve_sycl.cpp:53: warning: Member mode (typedef) of file pme_solve_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spread_sycl.cpp:436: warning: Member INSTANTIATE_2(order, numGrids, threadsPerAtom, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_spread_sycl.cpp:442: warning: Member INSTANTIATE(order, subGroupSize) (macro definition) of file pme_spread_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp:429: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:108: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:115: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:414: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:173: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:85: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:414: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp:429: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft.cpp:293: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:251: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:263: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:267: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:62: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:64: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:115: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:124: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:73: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:74: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:76: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:77: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/xvgio.cpp:63: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:97: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:511: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:512: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:513: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/device_stream_sycl.cpp:52: warning: Member makeQueuePropertyList(bool enableProfiling, DeviceStreamPriority priority) (function) of file device_stream_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/devicebuffer_ocl.h:386: warning: Member asMpiPointer(DeviceBuffer< ValueType > &) (function) of file devicebuffer_ocl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/devicebuffer_sycl.h:437: warning: Member asMpiPointer(DeviceBuffer< ValueType > &buffer) (function) of file devicebuffer_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gmxopencl.h:56: warning: Member CL_USE_DEPRECATED_OPENCL_2_0_APIS (macro definition) of file gmxopencl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:61: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:62: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:63: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:77: warning: unable to resolve reference to 'GpuEventSynchronizer::reset' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:79: warning: unable to resolve reference to 'GpuEventSynchronizer::consume' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:81: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:84: warning: unable to resolve reference to 'GpuEventSynchronizer::waitForEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:86: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:91: warning: unable to resolve reference to 'GpuEventSynchronizer::markEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:92: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gpueventsynchronizer.h:92: warning: unable to resolve reference to 'GpuEventSynchronizer::enqueueWaitEvent' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gputraits.h:63: warning: Member DeviceTexture (typedef) of file gputraits.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/gputraits_ocl.h:50: warning: Member DeviceTexture (typedef) of file gputraits_ocl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp:83: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *) (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc.cpp:88: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc_sycl.cpp:128: warning: Member pmallocSetDefaultDeviceContext(const DeviceContext *deviceContext) (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/pmalloc_sycl.cpp:137: warning: Member pmallocClearDefaultDeviceContext() (function) of file pmalloc_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:57: warning: Member SYCL_ASSERT(condition) (macro definition) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:78: warning: Member compilingForHost() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:94: warning: Member compilingForSubGroupSize() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:108: warning: Member skipKernelCompilation() (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:130: warning: Member atomicAddDefault(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:167: warning: Member atomicFetchAddLocal(T &val, const T delta) (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member __attribute__((always_inline)) static AmdPackedFloat3 operator*(const AmdPackedFloat3 &v (function) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:321: warning: Member s (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:325: warning: Member v (variable) of file sycl_kernel_utils.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp:66: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:68: warning: Member parseHardwareVersionNvidia(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:105: warning: Member getHardwareVersionNvidia(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:140: warning: Member parseHardwareVersionAmd(const std::string &archName) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:180: warning: Member getHardwareVersionAmd(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:214: warning: Member getHardwareVersionIntel(const sycl::device &device) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:250: warning: Member getDeviceGpuAwareMpiStatus(const sycl::backend backend) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl.cpp:543: warning: Member partitionDevices(const std::vector< sycl::device > &&devices) (function) of file device_management_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:51: warning: Member IntelProductConfig (enumeration) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:506: warning: Member getHardwareVersionFromIntelProductConfig(const IntelProductConfig productConfig) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:517: warning: Member getProductConfigFromPciExpressID(unsigned int pciExpressID) (function) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_management_sycl_intel_device_ids.cpp:129: warning: Member c_pciExpressIdsForProduct (variable) of file device_management_sycl_intel_device_ids.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp:1099: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp:1180: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp:162: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:61: warning: Member c_threadsPerBlock (variable) of file listed_forces_gpu_impl_gpu.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:113: warning: Member staggeredAtomicAddForce(sycl::global_ptr< Float3 > gm_f, Float3 f, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:134: warning: Member harmonic_gpu(const float kA, const float xA, const float x, sycl::private_ptr< float > V, sycl::private_ptr< float > F) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:152: warning: Member bonds_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:260: warning: Member bond_angle_gpu(const sycl::float4 xi, const sycl::float4 xj, const sycl::float4 xk, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< float > costh, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:279: warning: Member angles_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:347: warning: Member urey_bradley_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:460: warning: Member dih_angle_gpu(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< int > t3) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:489: warning: Member dih_angle_gpu_sincos(const T xi, const T xj, const T xk, const T xl, const PbcAiuc &pbcAiuc, sycl::private_ptr< Float3 > r_ij, sycl::private_ptr< Float3 > r_kj, sycl::private_ptr< Float3 > r_kl, sycl::private_ptr< Float3 > m, sycl::private_ptr< Float3 > n, sycl::private_ptr< int > t1, sycl::private_ptr< int > t2, sycl::private_ptr< float > cosval) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:529: warning: Member dopdihs_gpu(const float cpA, const float phiA, const int mult, const float phi, sycl::private_ptr< float > v, sycl::private_ptr< float > f) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:543: warning: Member do_dih_fup_gpu(const int i, const int j, const int k, const int l, const float ddphi, const Float3 r_ij, const Float3 r_kj, const Float3 r_kl, const Float3 m, const Float3 n, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const sycl::global_ptr< const Float4 > gm_xq, const int t1, const int t2, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:603: warning: Member pdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:649: warning: Member rbdihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:761: warning: Member idihs_gpu(const int i, sycl::private_ptr< float > vtot_loc, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_forceparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:814: warning: Member pairs_gpu(const int i, const sycl::global_ptr< const t_iatom > gm_forceatoms, const sycl::global_ptr< const t_iparams > gm_iparams, const sycl::global_ptr< const sycl::float4 > gm_xq, sycl::global_ptr< Float3 > gm_f, sycl::local_ptr< Float3 > sm_fShiftLoc, const PbcAiuc &pbcAiuc, const float scale_factor, sycl::private_ptr< float > vtotVdw_loc, sycl::private_ptr< float > vtotElec_loc, const int localId) (function) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:64: warning: Member c_deg2RadF (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:65: warning: Member c_Pi (variable) of file listed_forces_gpu_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/pairs.cpp:164: warning: Member sixthRoot(const real r) (function) of file pairs.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp:200: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp:148: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3080: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3082: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3098: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3109: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/functions.cpp:388: warning: Member IntegerTypes (typedef) of namespace anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:55: warning: Member jacobi(double **a, int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:65: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/nrjac.h:67: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/neldermead.cpp:97: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:52: warning: Member do_rotate(MatrixType a, int i, int j, int k, int l, double tau, double s) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:62: warning: Member jacobi(MatrixType a, const int n, double d[], MatrixType v) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:175: warning: Member jacobi(double **a, const int numDimensions, double *eigenvalues, double **eigenvectors, int *numRotations) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:185: warning: Member jacobi(gmx::ArrayRef< gmx::DVec > a, gmx::ArrayRef< double > eigenvalues, gmx::ArrayRef< gmx::DVec > eigenvectors) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/nrjac.cpp:194: warning: Member m_inv_gen(const real *m, int n, real *minv) (function) of file nrjac.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/optimization.cpp:60: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp:85: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp:156: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:84: warning: Member pvEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:86: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.h:88: warning: Member virialEnergyFieldNames (variable) of file energyoutput.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/gpuforcereduction.h:62: warning: Member HAVE_GPU_FORCE_REDUCTION (macro definition) of file gpuforcereduction.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:451: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constrtestrunners.h:58: warning: Member GPU_CONSTRAINTS_SUPPORTED (macro definition) of file constrtestrunners.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:93: warning: Member boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:95: warning: Member tricl_boxs_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:98: warning: Member vol_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:100: warning: Member dens_nm[] (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:102: warning: Member pvEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:104: warning: Member enthalpyEnergyFieldName (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:106: warning: Member virialEnergyFieldNames (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:110: warning: Member boxvel_nm (variable) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/energyoutput.cpp:123: warning: Member haveFepLambdaMoves(const t_inputrec &inputrec) (function) of file energyoutput.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/freeenergyparameters.cpp:58: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/leapfrogtestrunners.h:59: warning: Member GPU_LEAPFROG_SUPPORTED (macro definition) of file leapfrogtestrunners.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/settletestrunners.h:57: warning: Member GPU_SETTLE_SUPPORTED (macro definition) of file settletestrunners.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_impl.cpp:69: warning: Member sc_haveGpuConstraintSupport (variable) of file update_constrain_gpu_impl.cpp is not documented. warning: Include graph for 'md.cpp' not generated, too many nodes (71), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'mimic.cpp' not generated, too many nodes (54), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:170: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:172: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:175: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. warning: Include graph for 'rerun.cpp' not generated, too many nodes (57), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/rerun.cpp:111: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. warning: Include graph for 'runner.cpp' not generated, too many nodes (96), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp:72: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp:73: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:182: warning: Member gmx_sumd_sim(int gmx_unused nr, double gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:191: warning: Member gmx_sumf_sim(int gmx_unused nr, float gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:200: warning: Member gmx_sumi_sim(int gmx_unused nr, int gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:209: warning: Member gmx_sumli_sim(int gmx_unused nr, int64_t gmx_unused r[], const gmx_multisim_t gmx_unused *ms) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/multisim.cpp:387: warning: Member multisim_int_all_are_equal(const gmx_multisim_t *ms, int64_t value) (function) of file multisim.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:69: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:86: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:100: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:121: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:142: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:66: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp:55: warning: Member c_forces (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:60: warning: Member c_numLambdas (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:62: warning: Member dhdlVdw (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:63: warning: Member dhdlCoul (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:65: warning: Member dhdlLinearZero (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp:139: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:179: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:165: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/mttk.cpp:282: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:294: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:733: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:742: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:749: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:755: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:881: warning: Member getConnection(Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp:122: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp:135: warning: Member getGridOffset(gmx::ArrayRef< const Grid > grids, int gridIndex) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernel_common.h:90: warning: Member EnergyOutput (enumeration) of file kernel_common.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:50: warning: Member nbnxn_kernel_ElecRF_VdwLJFsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:51: warning: Member nbnxn_kernel_ElecRF_VdwLJPsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:52: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:53: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:54: warning: Member nbnxn_kernel_ElecQSTab_VdwLJ_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:55: warning: Member nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:56: warning: Member nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:57: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:58: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:59: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:60: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:61: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:62: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:63: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:65: warning: Member nbnxn_kernel_ElecRF_VdwLJ_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:66: warning: Member nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:67: warning: Member nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:68: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:69: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:70: warning: Member nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:71: warning: Member nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:72: warning: Member nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:73: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:74: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:75: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:76: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:77: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:78: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:79: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:81: warning: Member nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:82: warning: Member nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:83: warning: Member nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:84: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:85: warning: Member nbnxn_kernel_ElecRF_VdwLJEwCombLB_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:86: warning: Member nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:87: warning: Member nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:88: warning: Member nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:89: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:90: warning: Member nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:91: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:92: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:93: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:94: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_reference/kernel_ref.h:95: warning: Member nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (variable) of file kernel_ref.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:63: warning: Member nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid &grid, NbnxmGpu *nb, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const gmx::AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:83: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:97: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:128: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:178: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:202: warning: Member initPlistSorting(gpuPlistSorting *sorting) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:225: warning: Member init_plist(gpu_plist *pl) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:253: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:302: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:356: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:442: warning: Member gpu_init(const gmx::DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:511: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:528: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:689: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:792: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:823: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:829: warning: Member setupGpuShortRangeWork(NbnxmGpu *nb, const gmx::ListedForcesGpu *listedForcesGpu, const gmx::InteractionLocality iLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:842: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const gmx::InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:981: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1076: warning: Member nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1286: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1292: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp:355: warning: Member getENbnxnInitCombRule(const t_forcerec &forcerec) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_simd.h:115: warning: Member GMX_HAVE_NBNXM_SIMD_4XM (macro definition) of file nbnxm_simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistparams.h:73: warning: Member c_gpuNumClusterPerCellY (variable) of file pairlistparams.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlistparams.h:74: warning: Member c_gpuNumClusterPerCellX (variable) of file pairlistparams.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_gpu_buffer_ops_internal_sycl.cpp:50: warning: Member mode (typedef) of file nbnxm_gpu_buffer_ops_internal_sycl.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:52: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_8 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:53: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_32 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.h:54: warning: Member SYCL_NBNXM_SUPPORTS_SUBGROUP_SIZE_64 (macro definition) of file nbnxm_sycl_kernel.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:72: warning: Member FCiFloat3 (typedef) of file nbnxm_sycl_kernel_body.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:125: warning: Member mode (typedef) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:106: warning: Member elecEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:109: warning: Member elecEwaldTab (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:112: warning: Member ljEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_pruneonly.cpp:53: warning: Member mode (typedef) of file nbnxm_sycl_kernel_pruneonly.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/exclusions.cpp:200: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:98: warning: Member GENERATE_REFERENCE_DATA (macro definition) of file kernel_test.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:505: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:530: warning: Member makeRefDataFileName() (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:203: warning: Member c_numEnergyGroups (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:461: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:467: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:783: warning: Member testKernelTypes (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/com.cpp:118: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/pbc_aiuc_sycl.h:50: warning: Member xyzToShiftIndex(int x, int y, int z) (function) of file pbc_aiuc_sycl.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc.cpp:1421: warning: Member putAtomsInBoxTemplated(PbcType pbcType, const matrix box, const matrix boxDeformation, gmx::ArrayRef< gmx::RVec > x, gmx::ArrayRef< gmx::RVec > v) (function) of file pbc.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/pbc_simd.cpp:52: warning: Member set_pbc_simd(const t_pbc gmx_unused *pbc, real gmx_unused *pbc_simd) (function) of file pbc_simd.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp:173: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp:79: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:2017: warning: found documented return type for analyze_static that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:1832: warning: found documented return type for evaluate_boolean_static_part that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:1754: warning: found documented return type for init_method that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/compiler.cpp:1701: warning: found documented return type for process_const that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1025: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1140: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:482: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:915: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:880: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:965: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1003: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1076: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:599: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:539: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:564: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:752: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:717: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1025: warning: found documented return type for _gmx_sel_evaluate_and that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1140: warning: found documented return type for _gmx_sel_evaluate_arithmetic that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:482: warning: found documented return type for _gmx_sel_evaluate_children that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:915: warning: found documented return type for _gmx_sel_evaluate_method that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:880: warning: found documented return type for _gmx_sel_evaluate_method_params that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:965: warning: found documented return type for _gmx_sel_evaluate_modifier that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1003: warning: found documented return type for _gmx_sel_evaluate_not that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:1076: warning: found documented return type for _gmx_sel_evaluate_or that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.h:102: warning: found documented return type for _gmx_sel_evaluate_root that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.h:122: warning: found documented return type for _gmx_sel_evaluate_static that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:599: warning: found documented return type for _gmx_sel_evaluate_subexpr that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:539: warning: found documented return type for _gmx_sel_evaluate_subexpr_simple that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:564: warning: found documented return type for _gmx_sel_evaluate_subexpr_staticeval that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:752: warning: found documented return type for _gmx_sel_evaluate_subexprref that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:717: warning: found documented return type for _gmx_sel_evaluate_subexprref_simple that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/params.cpp:895: warning: found documented return type for parse_values_enum that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_compare.cpp:357: warning: found documented return type for convert_real_int that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_compare.cpp:119: warning: found documented return type for init_compare that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_distance.cpp:96: warning: found documented return type for init_common that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_distance.cpp:114: warning: found documented return type for init_frame_common that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:248: warning: found documented return type for init_insolidangle that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_keywords.cpp:345: warning: found documented return type for init_kweval that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_keywords.cpp:105: warning: found documented return type for init_kwreal that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_keywords.cpp:357: warning: found documented return type for init_output_kweval that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_merge.cpp:71: warning: found documented return type for init_merge that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_permute.cpp:82: warning: found documented return type for init_permute that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_position.cpp:94: warning: found documented return type for init_cog that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_position.cpp:104: warning: found documented return type for init_com that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_position.cpp:81: warning: found documented return type for init_kwpos that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_position.cpp:114: warning: found documented return type for init_output_pos that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_same.cpp:113: warning: found documented return type for init_same that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_simple.cpp:83: warning: found documented return type for check_molecules that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_simple.cpp:153: warning: found documented return type for check_pdbinfo that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:647: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:658: warning: Member GMX_SIMD4N_FLOAT_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:693: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:704: warning: Member GMX_SIMD4N_DOUBLE_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:738: warning: Member GMX_SIMD_HAVE_4NSIMD_UTIL_REAL (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:747: warning: Member GMX_SIMD4N_REAL_WIDTH (macro definition) of file simd.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:746: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:517: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:523: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:541: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:547: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:633: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:662: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:666: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:670: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:708: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:712: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:716: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:379: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:484: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/forcetable.h:79: warning: Member TableFormat (enumeration) of file forcetable.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:165: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:172: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:118: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:116: warning: Member nthreads_omp_faster_Nehalem (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:117: warning: Member nthreads_omp_faster_Intel_AVX (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:118: warning: Member nthreads_omp_faster_AMD_Ryzen (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:125: warning: Member nthreads_omp_faster_gpu_fac (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:135: warning: Member nthreads_omp_mpi_ok_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:136: warning: Member nthreads_omp_mpi_ok_min_cpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:137: warning: Member nthreads_omp_mpi_ok_min_gpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:138: warning: Member nthreads_omp_mpi_target_max (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/resourcedivision.cpp:142: warning: Member c_maxAutoTmpiRanksPerGpu (variable) of file resourcedivision.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include/gromacs/timing/instrumentation.h:216: warning: Member traceRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/include/gromacs/timing/instrumentation.h:217: warning: Member traceSubRangeStart(gmx_unused const char *rangeName, gmx_unused int rangeId) (function) of file instrumentation.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/trjconv.cpp:155: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:212: warning: Member gmx_mtop_atomloop_block_t (typedef) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:216: warning: Member gmx_mtop_atomloop_block_init(const gmx_mtop_t &mtop) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/include/gromacs/topology/mtop_atomloops.h:231: warning: Member gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop, const t_atom **atom, int *nmol) (function) of file mtop_atomloops.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/symtab.cpp:326: warning: Member close_symtab(t_symtab gmx_unused *symtab) (function) of file symtab.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:192: warning: Member SimulationParticleTestParameters (typedef) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:124: warning: Member checkParticleValue(TestReferenceChecker *checker, bool haveBState, const T &valueA, const T &valueB, const std::string &fieldName) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:137: warning: Member checkParticleMiscInfo(TestReferenceChecker *checker, ParticleType type, gmx::Index resind, int atomnumber, const std::string &elem) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:150: warning: Member checkParticle(TestReferenceChecker *checker, const SimulationParticle &particle) (function) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:195: warning: Member testParticleMassOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:196: warning: Member testParticleMassTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:197: warning: Member testParticleChargeOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:198: warning: Member testParticleChargeTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:199: warning: Member testParticleTypeValueOneState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/atoms.cpp:200: warning: Member testParticleTypeValueTwoState (variable) of file atoms.cpp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:67: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:74: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:81: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:95: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:73: warning: Member DsspTestParamsDsspNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:74: warning: Member DsspTestParamsGromacsNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:75: warning: Member DsspTestParamsDsspNoNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParamsGromacsNoNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:70: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:169: warning: Member DonorType (enumeration) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:163: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:165: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:167: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/hbond.cpp:70: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/scattering.cpp:68: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/cstringutil.cpp:100: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. warning: Included by graph for 'fatalerror.h' not generated, too many nodes (104), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:217: warning: Member gmx_call(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:218: warning: Member gmx_comm(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:219: warning: Member gmx_file(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:220: warning: Member gmx_impl(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:221: warning: Member gmx_incons(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:222: warning: Member gmx_input(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:223: warning: Member gmx_mem(msg) (macro definition) of file fatalerror.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/fatalerror.h:224: warning: Member gmx_open(fn) (macro definition) of file fatalerror.h is not documented. warning: Included by graph for 'gmxmpi.h' not generated, too many nodes (54), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:64: warning: Member ivec[3] (typedef) of file iserializer.h is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. warning: Included by graph for 'textwriter.h' not generated, too many nodes (53), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:70: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:71: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:72: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:73: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:74: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:76: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:77: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:79: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found warning: Included by graph for 'gmxpre.h' not generated, too many nodes (739), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:113: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:114: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:68: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:82: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:116: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:75: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:89: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:288: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:384: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/normalmodes.cpp:168: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp:96: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp:404: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simple_mdrun.cpp:191: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:61: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:74: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:87: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:108: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.h:60: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:61: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:74: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:87: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:108: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:416: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:416: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/virtualsites.cpp:86: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. warning: Included by graph for 'cmdlinetest.h' not generated, too many nodes (65), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'refdata.h' not generated, too many nodes (106), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testasserts.h' not generated, too many nodes (164), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testfilemanager.h' not generated, too many nodes (62), threshold is 50. Consider increasing DOT_GRAPH_MAX_NODES. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:95: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:105: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:333: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:246: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:254: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:262: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:304: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:339: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initOptions()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::optionsFinished()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::initAfterFirstFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishAnalysis()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::writeOutput()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::startFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::analyzeFrame()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command :0: warning: unable to resolve reference to 'gmx::EnergyAnalysisModule::finishFrames()' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:151: warning: unable to resolve reference to 'c_simdBestPairAlignmentFloat' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_float.h:152: warning: unable to resolve reference to 'c_simdBestPairAlignmentDouble' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/impl_reference/impl_reference_util_double.h:171: warning: @copydetails or @copydoc target 'c_simdBestPairAlignmentFloat' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:118: warning: @copydetails or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:184: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:99: warning: @copydetails or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:143: warning: @copydetails or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:119: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:113: warning: @copydetails or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/errorcodes.h:111: warning: explicit link request to 'eeUnknownError' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:179: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:401: warning: @copydetails or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:418: warning: @copydetails or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:82: warning: @copydetails or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:189: warning: @copydetails or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selection.h:36: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((ext_vector_type(2))) Native_float2_ (typedef) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:214: warning: Member __attribute__((packed)) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:240: warning: Member __attribute__((always_inline)) float operator[](Index i) const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:250: warning: Member __attribute__((always_inline)) float &operator[](Index i) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:260: warning: Member __attribute__((always_inline)) float x() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:261: warning: Member __attribute__((always_inline)) float y() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:262: warning: Member __attribute__((always_inline)) Native_float2_ xy() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:263: warning: Member __attribute__((always_inline)) float z() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:267: warning: Member AmdPackedFloat3(float x, float y, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:269: warning: Member AmdPackedFloat3(Native_float2_ xy, float z) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:271: warning: Member AmdPackedFloat3(Float3 r) (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/sycl_kernel_utils.h:273: warning: Member operator Float3() const (function) of struct AmdPackedFloat3 is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/constraint_gpu_helpers.h:51: warning: Member AtomsAdjacencyListElement(int indexOfSecondConstrainedAtom, int indexOfConstraint, int signFactor) (function) of struct AtomsAdjacencyListElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/dlbtiming.h:215: warning: Member impl_ (variable) of class BalanceRegion is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_internal.h:112: warning: Member GMX_DISALLOW_COPY_MOVE_AND_ASSIGN(bonded_threading_t) (function) of struct bonded_threading_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:436: warning: Member mtop (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:437: warning: Member effectiveAtomDensity (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:438: warning: Member inputrec (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:439: warning: Member pressureTolerance (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:440: warning: Member listSetup (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:441: warning: Member useGpuList (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist_tuning.cpp:442: warning: Member mtsFactor (variable) of struct CalcVerletBufferParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:176: warning: Member supportedSubGroupSizes() const (function) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:175: warning: Member supportedSubGroupSizesSize (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/device_information.h:181: warning: Member gpuAwareMpiStatus (variable) of struct DeviceInformation is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:66: warning: Member bUse (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:67: warning: Member comm_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:68: warning: Member rank_intra (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/commrec.h:69: warning: Member comm_inter (variable) of struct gmx_nodecomm_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:121: warning: Member ewaldcoeff_q (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:122: warning: Member ewaldcoeff_lj (variable) of struct gmx_pme_comm_n_box_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:137: warning: Member vir_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:138: warning: Member energy_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:139: warning: Member energy_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:140: warning: Member dvdlambda_q (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_pp_communication.h:141: warning: Member dvdlambda_lj (variable) of struct gmx_pme_comm_vir_ene_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:107: warning: Member gmx_pme_pp(MPI_Comm simulationCommunicator, std::vector< PpRanks > &&ppRanks) (function) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:114: warning: Member chargeB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:115: warning: Member sqrt_c6A (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:116: warning: Member sqrt_c6B (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:117: warning: Member sigmaA (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:118: warning: Member sigmaB (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_only.cpp:125: warning: Member stat (variable) of struct gmx_pme_pp is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:146: warning: Member cyclic (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:147: warning: Member order (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:148: warning: Member tmpswap (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:149: warning: Member incycle (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:150: warning: Member bEx (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:156: warning: Member Epot (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:157: warning: Member beta (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:158: warning: Member Vol (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/replicaexchange.cpp:159: warning: Member de (variable) of struct gmx_repl_ex is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:68: warning: Member aj() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:69: warning: Member ak() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:70: warning: Member al() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:71: warning: Member am() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:73: warning: Member c0() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:74: warning: Member c1() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:75: warning: Member c2() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/grompp_impl.h:77: warning: Member interactionTypeName() const (function) of class InteractionOfType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:144: warning: Member kernel_noener_noprune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:145: warning: Member kernel_ener_noprune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:146: warning: Member kernel_noener_prune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:147: warning: Member kernel_ener_prune_ptr[Nbnxm::c_numElecTypes][Nbnxm::c_numVdwTypes] (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:157: warning: Member kernel_memset_f (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:158: warning: Member kernel_memset_f2 (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/opencl/nbnxm_ocl_types.h:159: warning: Member kernel_memset_f3 (variable) of struct NbnxmGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm.h:482: warning: Member setupFepThreadedForceBuffer(int numAtomsForce) (function) of struct nonbonded_verlet_t is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/pairlist.h:241: warning: Member PackedJClusterList(const gmx::PinningPolicy pinningPolicy) (function) of class PackedJClusterList is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_types_host.h:263: warning: Member useNvshmem (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_types_host.h:265: warning: Member nvshmemParams (variable) of struct PmeGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:176: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(PmeGpuProgramImpl) (function) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:115: warning: Member splineKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:116: warning: Member splineKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:117: warning: Member spreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:118: warning: Member spreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:119: warning: Member splineAndSpreadKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:120: warning: Member splineAndSpreadKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:121: warning: Member splineAndSpreadKernelWriteSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:122: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:123: warning: Member splineKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:124: warning: Member splineKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:125: warning: Member spreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:126: warning: Member spreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:127: warning: Member splineAndSpreadKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:128: warning: Member splineAndSpreadKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:129: warning: Member splineAndSpreadKernelWriteSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:130: warning: Member splineAndSpreadKernelWriteSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:143: warning: Member gatherKernelSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:144: warning: Member gatherKernelThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:145: warning: Member gatherKernelReadSplinesSingle (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:146: warning: Member gatherKernelReadSplinesThPerAtom4Single (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:147: warning: Member gatherKernelDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:148: warning: Member gatherKernelThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:149: warning: Member gatherKernelReadSplinesDual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:150: warning: Member gatherKernelReadSplinesThPerAtom4Dual (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:160: warning: Member solveYZXKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:161: warning: Member solveXYZKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:162: warning: Member solveYZXEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:163: warning: Member solveXYZEnergyKernelA (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:164: warning: Member solveYZXKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:165: warning: Member solveXYZKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:166: warning: Member solveYZXEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:167: warning: Member solveXYZEnergyKernelB (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_program_impl.h:169: warning: Member nvshmemSignalKern (variable) of struct PmeGpuProgramImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tables/forcetable.h:88: warning: Member t_forcetable(TableInteraction interaction, TableFormat format) (function) of struct t_forcetable is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/fcdata.h:216: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(t_oriresdata) (function) of struct t_oriresdata is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:213: warning: Member fnTpr (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:213: warning: Member fnPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:213: warning: Member fnCoordSel (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:215: warning: Member bPullf (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:216: warning: Member tmin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:216: warning: Member tmax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:228: warning: Member min (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:228: warning: Member max (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:228: warning: Member dz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:229: warning: Member Temperature (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:245: warning: Member bBoundsOnly (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:256: warning: Member bTauIntGiven (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:267: warning: Member bHistEq (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:293: warning: Member bsMethod (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:296: warning: Member tauBootStrap (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:300: warning: Member histBootStrapBlockLength (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:306: warning: Member bs_verbose (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:312: warning: Member bTab (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabX (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabY (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabMin (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabMax (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:313: warning: Member tabDz (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxana/gmx_wham.cpp:314: warning: Member tabNbins (variable) of struct UmbrellaOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp:89: warning: Member aj() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp:90: warning: Member ak() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp:91: warning: Member al() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/vsite_parm.cpp:93: warning: Member parameterValue() const (function) of class VsiteBondedInteraction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:71: warning: Member WarningHandler(bool allowWarnings, int maxNumberWarnings) (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:89: warning: Member errorCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:91: warning: Member warningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:93: warning: Member noteCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/warninp.h:95: warning: Member maxWarningCount() const (function) of class WarningHandler is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:144: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/options/abstractoptionstorage.h:145: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3080: warning: Member CmapForceStructure (typedef) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3082: warning: Member processCmapForceComponent(const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3098: warning: Member applyCmapForceComponent(const gmx::RVec forceComponent) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/bonded.cpp:3109: warning: Member accumulateCmapForces(const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2) (function) of namespace anonymous_namespace{bonded.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:112: warning: Member NonbondedFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:113: warning: Member UpdateFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:114: warning: Member PmeFlavor (typedef) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:68: warning: Member ElectrostaticsFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:82: warning: Member CouplingFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:97: warning: Member OffloadFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:116: warning: Member SeparatePmeRankFlavor (enumeration) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:75: warning: Member enumValueToString(const ElectrostaticsFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:89: warning: Member enumValueToString(const CouplingFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:104: warning: Member enumValueToString(const OffloadFlavor enumValue) (function) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:288: warning: Member sc_mdpFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/domain_decomposition.cpp:384: warning: Member sc_offloadFlavors (variable) of namespace anonymous_namespace{domain_decomposition.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/freeenergydispatch.cpp:146: warning: Member dispatchFreeEnergyKernel(gmx::ArrayRef< const std::unique_ptr< t_nblist > > nbl_fep, const gmx::ArrayRefWithPadding< const gmx::RVec > &coords, bool useSimd, int ntype, const interaction_const_t &ic, gmx::ArrayRef< const gmx::RVec > shiftvec, gmx::ArrayRef< const real > nbfp, gmx::ArrayRef< const real > nbfp_grid, gmx::ArrayRef< const real > chargeA, gmx::ArrayRef< const real > chargeB, gmx::ArrayRef< const int > typeA, gmx::ArrayRef< const int > typeB, gmx::ArrayRef< const real > lambda, const bool clearForcesAndEnergies, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForceBuffer, gmx::ThreadedForceBuffer< gmx::RVec > *threadedForeignEnergyBuffer, gmx_grppairener_t *foreignGroupPairEnergies, gmx_enerdata_t *enerd, const gmx::StepWorkload &stepWork, t_nrnb *nrnb) (function) of namespace anonymous_namespace{freeenergydispatch.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/functions.cpp:388: warning: Member IntegerTypes (typedef) of namespace anonymous_namespace{functions.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/indexutil.cpp:91: warning: Member setGroup(const int(&atoms)[count]) (function) of class anonymous_namespace{indexutil.cpp}::IndexBlockTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/minimize.cpp:915: warning: Member mdModulesNotifiers (variable) of class anonymous_namespace{minimize.cpp}::EnergyEvaluator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:124: warning: Member AspartateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:146: warning: Member GlutamateStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:168: warning: Member GlutamineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:190: warning: Member LysineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:211: warning: Member ArginineStates (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1274: warning: Member ChainSeparationType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1533: warning: Member VSitesType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1544: warning: Member WaterType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1560: warning: Member MergeType (enumeration) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:105: warning: Member res2bb_notermini(const std::string &name, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:116: warning: Member enumValueToLongString(HistidineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:131: warning: Member enumValueToString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:138: warning: Member enumValueToLongString(AspartateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:153: warning: Member enumValueToString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:160: warning: Member enumValueToLongString(GlutamateStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:175: warning: Member enumValueToString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:182: warning: Member enumValueToLongString(GlutamineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:197: warning: Member enumValueToString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:203: warning: Member enumValueToLongString(LysineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:218: warning: Member enumValueToString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:225: warning: Member enumValueToLongString(ArginineStates enumValue) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:234: warning: Member select_res(int resnr, const char *title, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:256: warning: Member get_asptp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:261: warning: Member get_glutp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:266: warning: Member get_glntp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:271: warning: Member get_lystp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:276: warning: Member get_argtp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:281: warning: Member get_histp(int resnr, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:286: warning: Member read_rtprename(const char *fname, FILE *fp, std::vector< RtpRename > *rtprename) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:344: warning: Member search_resrename(gmx::ArrayRef< const RtpRename > rr, const char *name, bool bStart, bool bEnd, bool bCompareFFRTPname) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:387: warning: Member rename_resrtp(t_atoms *pdba, int nterpairs, gmx::ArrayRef< const int > r_start, gmx::ArrayRef< const int > r_end, gmx::ArrayRef< const RtpRename > rr, t_symtab *symtab, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:445: warning: Member pdbres_to_gmxrtp(t_atoms *pdba) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:458: warning: Member rename_pdbres(t_atoms *pdba, const char *oldnm, const char *newnm, bool bFullCompare, t_symtab *symtab) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:553: warning: Member check_occupancy(t_atoms *atoms, const char *filename, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:616: warning: Member write_posres(const char *fn, t_atoms *pdba, real fc) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:645: warning: Member read_pdball(const char *inf, bool bOutput, const char *outf, char **title, t_atoms *atoms, rvec **x, PbcType *pbcType, matrix box, bool bRemoveH, t_symtab *symtab, const ResidueTypeMap &residueTypeMap, const char *watres, AtomProperties *aps, bool bVerbose) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:719: warning: Member process_chain(const gmx::MDLogger &logger, t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bTrpU, bool bPheU, bool bTyrU, bool bLysMan, bool bAspMan, bool bGluMan, bool bHisMan, bool bArgMan, bool bGlnMan, real angle, real distance, t_symtab *symtab, gmx::ArrayRef< const RtpRename > rr) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:809: warning: Member pdbicomp(const t_pdbindex &a, const t_pdbindex &b) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:827: warning: Member sort_pdbatoms(gmx::ArrayRef< const PreprocessResidue > restp_chain, int natoms, t_atoms **pdbaptr, t_atoms **newPdbAtoms, std::vector< gmx::RVec > *x) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:913: warning: Member remove_duplicate_atoms(t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bVerbose, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:985: warning: Member checkResidueTypeSanity(t_atoms *pdba, int r0, int r1, const ResidueTypeMap &residueTypeMap) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1059: warning: Member find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, const ResidueTypeMap &residueTypeMap, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1294: warning: Member modify_chain_numbers(t_atoms *pdba, ChainSeparationType chainSeparation, const gmx::MDLogger &logger) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1418: warning: Member checkChainCyclicity(t_atoms *pdba, rvec *pdbx, int start_ter, int end_ter, gmx::ArrayRef< const PreprocessResidue > rtpFFDB, gmx::ArrayRef< const RtpRename > rr, real long_bond_dist_, real short_bond_dist_) (function) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1283: warning: Member c_chainSeparationTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1286: warning: Member c_chainSeparationTypeNotificationMessages (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1540: warning: Member c_vsitesTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1556: warning: Member c_waterTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/pdb2gmx.cpp:1567: warning: Member c_mergeTypeNames (variable) of namespace anonymous_namespace{pdb2gmx.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:74: warning: Member assertIsFinite(Float3 gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_gpu_calculate_splines_sycl.h:82: warning: Member assertIsFinite(T gmx_unused arg) (function) of namespace anonymous_namespace{pme_gpu_calculate_splines_sycl.h} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp:94: warning: Member c_currentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/state.cpp:199: warning: Member c_dfHistoryCurrentVersion (variable) of namespace anonymous_namespace{state.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:875: warning: Member mode (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/optionflags.h:107: warning: explicit link request to 'OptionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectionenums.h:82: warning: explicit link request to 'SelectionFlag' could not be resolved /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:131: warning: Member ClCommandQueue (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:132: warning: Member ClProgram (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/oclraii.h:133: warning: Member ClKernel (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:63: warning: Member packSendBufKernel(Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:117: warning: Member launchPackSendBufKernel(const DeviceStream &deviceStream, int xSendSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange_impl_gpu_sycl.cpp:131: warning: Member launchUnpackRecvBufKernel(const DeviceStream &deviceStream, int fRecvSize, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_cufftmp.cpp:102: warning: Member handleCufftError(cufftResult_t status, const char *msg) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:251: warning: Member launchVkFft(const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/massrepartitioning.cpp:44: warning: Member smallestAtomMass(const gmx_mtop_t &mtop) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:70: warning: Member simdString(SimdType s) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/simd_support.cpp:199: warning: Member simdCompiled() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_impl_gpu.cpp:67: warning: Member chooseSubGroupSizeForDevice(const DeviceInformation &deviceInfo) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/listed_forces_gpu_internal_sycl.cpp:878: warning: Member bondedKernel(sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/leapfrog_gpu_internal_sycl.cpp:169: warning: unable to resolve reference to 'NumTempScaleValues' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs_gpu_internal_sycl.cpp:451: warning: Member launchLincsKernel(const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&... args) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:733: warning: Member hasStartVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:742: warning: Member hasEndVelocityScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:749: warning: Member hasPositionScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:755: warning: Member hasParrinelloRahmanScaling() (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:881: warning: Member getConnection(Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:125: warning: Member doCheckpointData(CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_2xmm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:62: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:74: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:86: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:98: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:110: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:122: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:134: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:146: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:158: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:170: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:182: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:194: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:206: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:218: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:230: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:242: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:254: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:266: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:278: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:290: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:302: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:314: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:326: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:338: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:350: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:362: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:374: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:386: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:398: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:410: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:423: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:435: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:447: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:459: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:471: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:483: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:495: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:507: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:519: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:531: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:543: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:555: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:567: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:579: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:591: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:603: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:615: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:627: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:639: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:651: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:663: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:675: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:687: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:699: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:711: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:723: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:735: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:747: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:759: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:771: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:784: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:796: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:808: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:820: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:832: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:844: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:856: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:868: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:880: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:892: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:904: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:916: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:928: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:940: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:952: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:964: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:976: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:988: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1000: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1012: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1024: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1036: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1048: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1060: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1072: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1084: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1096: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1108: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1120: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/kernels_simd_4xm/kernels.h:1132: warning: Member nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs >(const NbnxnPairlistCpu *nbl, const nbnxn_atomdata_t *nbat, const interaction_const_t *ic, const rvec *shift_vec, nbnxn_atomdata_output_t *out) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/selectioncollection.cpp:964: warning: Member swap(SelectionCollection &lhs, SelectionCollection &rhs) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:165: warning: Member decideWhetherToUseGpusForPmeFft(const TaskTarget pmeFftTarget) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:172: warning: Member canUseGpusForPme(const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:112: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:118: warning: @copybrief or @copydoc target 'fromString(const char *)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:178: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:183: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:188: warning: @copybrief or @copydoc target 'intToString(int)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/stringutil.cpp:132: warning: Member formatString(gmx_fmtstr const char *fmt,...) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:400: warning: @copybrief or @copydoc target 'replaceAll(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:417: warning: @copybrief or @copydoc target 'replaceAllWords(const std::string &, const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:81: warning: @copybrief or @copydoc target 'startsWith(const std::string &, const std::string &)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:98: warning: @copybrief or @copydoc target 'endsWith(const char *, const char *)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:117: warning: @copybrief or @copydoc target 'contains(const std::string &str, const char *substr)' not found /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:142: warning: @copybrief or @copydoc target 'endsWith(const std::string &str, const char *suffix)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:120: warning: Member globalSimulationState(const SimulationInput &) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:121: warning: Member applyGlobalInputRecord(const SimulationInput &, t_inputrec *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinput.h:122: warning: Member applyGlobalTopology(const SimulationInput &, gmx_mtop_t *) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:200: warning: Member toString(bool t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:204: warning: Member toString(int t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:208: warning: Member toString(int64_t t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:212: warning: Member toString(float t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:216: warning: Member toString(double t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:220: warning: Member toString(unsigned char t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/strconvert.h:224: warning: Member toString(std::string t) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/vec.h:625: warning: Member norm2(T *v) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/tests/colvarsoptions.cpp:80: warning: Member colvarsConfig (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/forcebuffers.cpp:55: warning: Member c_forces (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/nosehooverchains.cpp:67: warning: Member nhcUsageNames (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:55: warning: Member c_centralShiftIndex (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:56: warning: Member c_numShiftVectors (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment/decidegpuusage.cpp:118: warning: Member c_gpuBuildSyclWithoutGpuFft (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:83: warning: Member c_angstrom (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:84: warning: Member c_kilo (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:85: warning: Member c_nano (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:86: warning: Member c_pico (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:87: warning: Member c_nm2A (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:88: warning: Member c_cal2Joule (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:89: warning: Member c_electronCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:91: warning: Member c_amu (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:92: warning: Member c_boltzmann (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:93: warning: Member c_avogadro (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:94: warning: Member c_universalGasConstant (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:95: warning: Member c_boltz (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:96: warning: Member c_faraday (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:97: warning: Member c_planck1 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:98: warning: Member c_planck (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:100: warning: Member c_epsilon0Si (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:102: warning: Member c_epsilon0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:105: warning: Member c_speedOfLight (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:108: warning: Member c_rydberg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:110: warning: Member c_one4PiEps0 (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:115: warning: Member c_barMdunits (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:116: warning: Member c_presfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:121: warning: Member c_debye2Enm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:122: warning: Member c_enm2Debye (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:126: warning: Member c_fieldfac (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:129: warning: Member c_hartree2Kj (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:130: warning: Member c_bohr2Nm (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:131: warning: Member c_hartreeBohr2Md (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:133: warning: Member c_rad2Deg (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/math/units.h:134: warning: Member c_deg2Rad (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:64: warning: Member sc_atomInfo_HasPerturbedCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:65: warning: Member sc_atomInfo_Exclusion (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:66: warning: Member sc_atomInfo_Constraint (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:67: warning: Member sc_atomInfo_Settle (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:68: warning: Member sc_atomInfo_BondCommunication (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:69: warning: Member sc_atomInfo_HasVdw (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/atominfo.h:70: warning: Member sc_atomInfo_HasCharge (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:44: warning: Member c_dBoxY (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:45: warning: Member c_dBoxX (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:379: warning: Member c_simdBestPairAlignment (variable) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:657: warning: Member Simd4NFloat (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:703: warning: Member Simd4NDouble (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:746: warning: Member Simd4NReal (typedef) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:517: warning: Member load(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:523: warning: Member load(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:541: warning: Member loadU(const std::enable_if_t< std::is_arithmetic_v< T >, T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:547: warning: Member loadU(const AlignedArray< internal::SimdTraitsT< T >, N > &m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:628: warning: Member load(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:633: warning: Member loadU(const internal::Simd4TraitsT< T > *m) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:662: warning: Member loadUNDuplicate4(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:666: warning: Member load4DuplicateN(const float *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:670: warning: Member loadU4NOffset(const float *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:708: warning: Member loadUNDuplicate4(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:712: warning: Member load4DuplicateN(const double *f) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:716: warning: Member loadU4NOffset(const double *f, int) (function) of namespace gmx is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:403: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:300: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:310: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:345: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:357: warning: unable to resolve reference to 'SimdBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdReal' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:358: warning: unable to resolve reference to 'SimdIBool' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:359: warning: unable to resolve reference to 'SimdInt32' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtB2IB' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:361: warning: unable to resolve reference to 'cvtIB2B' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/correlationhistory.h:61: warning: unable to resolve reference to 'updateCorrelationGridHistory' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:97: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:98: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:92: warning: @copybrief or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:93: warning: @copydetails or @copydoc target 'readKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:123: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:124: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:118: warning: @copybrief or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/checkpoint.h:119: warning: @copydetails or @copydoc target 'writeKvtCheckpointValue' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:62: warning: unable to resolve reference to 'ChangeAtomsType' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/requirements.cpp:58: warning: unable to resolve reference to 'ChangeSettingType' for \ref command /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:73: warning: Member formatSingleValue(const bool &value) const override (function) of class gmx::BooleanOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< bool > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/booltype.h:72: warning: Member value_ (variable) of struct gmx::BoolType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:69: warning: Member flag (variable) of struct gmx::CacheLineAlignedFlag is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/clfftinitializer.h:96: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(ClfftInitializer) (function) of class gmx::ClfftInitializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:78: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:81: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:89: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:78: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:81: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:89: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:78: warning: Member gmxPbc_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:81: warning: Member logger_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:88: warning: Member rng_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/colvars/colvarproxygromacs.h:89: warning: Member normalDistribution_ (variable) of class gmx::ColvarProxyGromacs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:101: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/computeglobalselement.cpp:377: warning: Member getElementPointerImpl(LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/computeglobalselement.cpp:411: warning: Member getElementPointerImpl(LegacySimulatorData *simulator, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer) (function) of class gmx::ComputeGlobalsElement is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:157: warning: Member coordinates_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:158: warning: Member box_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:159: warning: Member pbc_ (variable) of struct gmx::CoordinatesAndBoxPreprocessed is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/coordstate.h:84: warning: found documented return type for gmx::CoordState::sampleUmbrellaGridpoint that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:134: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:145: warning: Member force(const std::array< SimdReal, nR > &rSquaredV, const std::array< SimdReal, nR > gmx_unused &dummyRInvV, const std::array< SimdReal, nR > &rInvExclV, const std::array< SimdBool, nR > &withinCutoffV) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldAnalytical > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:194: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::EwaldTabulated > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_coulomb_functions.h:83: warning: Member CoulombCalculator(const interaction_const_t &ic) (function) of class gmx::CoulombCalculator< KernelCoulombType::RF > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:108: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:132: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_diagonal_masker.h:163: warning: Member DiagonalMasker(const nbnxn_atomdata_t::SimdMasks &simdMasks) (function) of class gmx::DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:134: warning: Member formatSingleValue(const double &value) const override (function) of class gmx::DoubleOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< double > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:251: warning: Member const_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:252: warning: Member reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:253: warning: Member const_reverse_iterator (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:275: warning: Member const_pointer (typedef) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:230: warning: Member operator[](const std::size_t arrayIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:236: warning: Member operator[](const EnumType enumIndex) (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:241: warning: Member operator[](const EnumType enumIndex) const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:259: warning: Member end() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:260: warning: Member begin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:261: warning: Member end() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:267: warning: Member rend() (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:268: warning: Member rbegin() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:269: warning: Member rend() const (function) of struct gmx::EnumerationArray is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/enumerationhelpers.h:182: warning: Member end() const (function) of class gmx::EnumerationWrapper is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:236: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::EnumOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/stringutil.h:440: warning: Member operator()(const std::string &lhs, const std::string &rhs) const (function) of class gmx::EqualCaseInsensitive is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/filenameoptionstorage.h:74: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::FileNameOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:162: warning: Member formatSingleValue(const float &value) const override (function) of class gmx::FloatOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< float > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:106: warning: Member homenr_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:107: warning: Member chargeA_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/iforceprovider.h:108: warning: Member massT_ (variable) of class gmx::ForceProviderInput is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:106: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:107: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:108: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:109: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:110: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:111: warning: Member context_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:112: warning: Member device_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:113: warning: Member commandQueue_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_ocl_vkfft.cpp:115: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplOclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_rocfft.cpp:360: warning: Member complexGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclRocfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:124: warning: Member configuration_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:125: warning: Member application_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:126: warning: Member launchParams_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:127: warning: Member bufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:128: warning: Member inputBufferSize_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:129: warning: Member queue_device_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/gpu_3dfft_sycl_vkfft.cpp:131: warning: Member realGrid_ (variable) of class gmx::Gpu3dFft::ImplSyclVkfft::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/gpuforcereduction.h:125: warning: Member registerForcesReadyNvshmemFlags(DeviceBuffer< uint64_t > syncObj) (function) of class gmx::GpuForceReduction is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange.h:100: warning: Member GpuHaloExchange(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/domdec/gpuhaloexchange.h:101: warning: Member operator=(GpuHaloExchange &&source) noexcept (function) of class gmx::GpuHaloExchange is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:115: warning: Member formatSingleValue(const int64_t &value) const override (function) of class gmx::Int64OptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int64_t > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:95: warning: Member formatSingleValue(const int &value) const override (function) of class gmx::IntegerOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:86: warning: Member doUChar(unsigned char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:87: warning: Member doChar(char *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:88: warning: Member doUShort(unsigned short *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:89: warning: Member doInt(int *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:90: warning: Member doInt32(int32_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:91: warning: Member doInt64(int64_t *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:92: warning: Member doFloat(float *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:93: warning: Member doDouble(double *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:94: warning: Member doReal(real *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:95: warning: Member doIvec(ivec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:96: warning: Member doRvec(rvec *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:97: warning: Member doString(std::string *value)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:98: warning: Member doOpaque(char *data, std::size_t size)=0 (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:112: warning: Member doCharArray(char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:119: warning: Member doUCharArray(unsigned char *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:126: warning: Member doUShortArray(unsigned short *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:133: warning: Member doIntArray(int *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:140: warning: Member doInt32Array(int32_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:147: warning: Member doInt64Array(int64_t *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:154: warning: Member doFloatArray(float *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:161: warning: Member doDoubleArray(double *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:168: warning: Member doRealArray(real *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:175: warning: Member doIvecArray(ivec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/iserializer.h:182: warning: Member doRvecArray(rvec *values, int elements) (function) of class gmx::ISerializer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:137: warning: Member value (variable) of struct gmx::IsSerializableEnum is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:124: warning: Member value (variable) of struct gmx::IsSerializableType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:143: warning: Member ddrank_opt_choices[static_cast< int >(DdRankOrder::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:148: warning: Member dddlb_opt_choices[static_cast< int >(DlbOption::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:153: warning: Member thread_aff_opt_choices[static_cast< int >(ThreadAffinity::Count)+1] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:158: warning: Member nbpu_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:159: warning: Member pme_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:160: warning: Member pme_fft_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:161: warning: Member bonded_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:162: warning: Member update_opt_choices[5] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:163: warning: Member devicesSelectedByUser (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:164: warning: Member userGpuTaskAssignment (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:167: warning: Member imdOptions (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/legacymdrunoptions.h:169: warning: Member pa[48] (variable) of class gmx::LegacyMdrunOptions is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:332: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:483: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:179: warning: Member LennardJonesCalculator(const interaction_const_t gmx_unused &ic) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:209: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< false, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:231: warning: Member LennardJonesCalculator(const interaction_const_t &ic) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/simd_lennardjones_functions.h:270: warning: Member forceSigmaEpsilon(const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, SimdBool *withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, SimdReal sixth, SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV) (function) of class gmx::LennardJonesCalculator< true, InteractionModifiers::PotShift > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:212: warning: Member tmpncc (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:213: warning: Member tmp1 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:214: warning: Member tmp2 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:215: warning: Member tmp3 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/lincs.cpp:216: warning: Member tmp4 (variable) of class gmx::Lincs is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.h:139: warning: Member Graph (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/mdgraph_gpu_impl.h:140: warning: Member GraphInstance (typedef) of class gmx::MdGpuGraph::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrunutility/mdmodulesnotifiers.h:85: warning: Member MDModulesAtomsRedistributedSignal(const matrix box, gmx::ArrayRef< const RVec > x) (function) of struct gmx::MDModulesAtomsRedistributedSignal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.h:145: warning: Member operator=(Mdrunner &&handle) noexcept (function) of class gmx::Mdrunner is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/runner.h:391: warning: Member operator=(MdrunnerBuilder &&builder) noexcept (function) of class gmx::MdrunnerBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:67: warning: Member MessageStringCollector(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/message_string_collector.h:68: warning: Member operator=(MessageStringCollector &&) noexcept (function) of class gmx::MessageStringCollector is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:218: warning: Member allocator_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:219: warning: Member size_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:220: warning: Member reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:221: warning: Member const_reference (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:222: warning: Member storage_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:223: warning: Member pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:224: warning: Member const_pointer (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:225: warning: Member iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:226: warning: Member const_iterator (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:227: warning: Member difference_type (typedef) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:351: warning: Member data() const noexcept (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:353: warning: Member begin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:354: warning: Member end() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:356: warning: Member cbegin() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:357: warning: Member cend() (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:359: warning: Member begin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:360: warning: Member end() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:362: warning: Member cbegin() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/include/gromacs/math/paddedvector.h:363: warning: Member cend() const (function) of class gmx::PaddedVector is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu.h:112: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/pme_force_sender_gpu_impl.h:132: warning: Member waitForEvents() (function) of class gmx::PmeForceSenderGpu::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmforceprovider.h:71: warning: Member QMMMForceProvider(const QMMMParameters ¶meters, const LocalAtomSet &localQMAtomSet, const LocalAtomSet &localMMAtomSet, PbcType pbcType, const MDLogger &logger) (function) of class gmx::QMMMForceProvider is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/qmmm/qmmmtypes.h:142: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(QMMMParameters) (function) of struct gmx::QMMMParameters is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:89: warning: Member operator=(const RestraintManager &)=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:90: warning: Member RestraintManager(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/manager.h:91: warning: Member operator=(RestraintManager &&) noexcept=default (function) of class gmx::RestraintManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/restraint/restraintmdmodule_impl.h:287: warning: Member operator=(RestraintMDModuleImpl &&) noexcept=default (function) of class gmx::RestraintMDModuleImpl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:101: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/scattering-debye.h:101: warning: Member getIntensity(size_t qi) (function) of class gmx::ComputeDebyeScattering is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:63: warning: Member ScalingMatrix(const Matrix3x3 &m) (function) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member xx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zz (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member yx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zx (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update_constrain_gpu_internal.h:67: warning: Member zy (variable) of struct gmx::ScalingMatrix is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:144: warning: Member SelectionCollection(const SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:145: warning: Member operator=(SelectionCollection rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/selection/selectioncollection.h:146: warning: Member swap(SelectionCollection &rhs) (function) of class gmx::SelectionCollection is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/evaluate.cpp:406: warning: found documented return type for gmx::SelectionEvaluator::evaluate that does not return anything /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/coordinateio/ioutputadapter.h:105: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(IOutputAdapter) (function) of class gmx::IOutputAdapter is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.h:139: warning: Member SimulationInputHandle(const SimulationInputHandle &source) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.h:140: warning: Member SimulationInputHandle(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.h:142: warning: Member operator=(const SimulationInputHandle &rhs) (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulationinputhandle.h:143: warning: Member operator=(SimulationInputHandle &&) noexcept=default (function) of class gmx::SimulationInputHandle is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:341: warning: Member add(MembedHolder &&membedHolder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:343: warning: Member add(std::unique_ptr< StopHandlerBuilder > stopHandlerBuilder) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:348: warning: Member add(SimulatorStateData &&simulatorStateData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:353: warning: Member add(SimulatorConfig &&simulatorConfig) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:360: warning: Member add(SimulatorEnv &&simulatorEnv) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:365: warning: Member add(Profiling &&profiling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:367: warning: Member add(ConstraintsParam &&constraintsParam) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:372: warning: Member add(LegacyInput &&legacyInput) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:377: warning: Member add(ReplicaExchangeParameters &&replicaExchangeParameters) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:379: warning: Member add(InteractiveMD &&interactiveMd) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:384: warning: Member add(SimulatorModules &&simulatorModules) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:389: warning: Member add(CenterOfMassPulling &¢erOfMassPulling) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:394: warning: Member add(IonSwapping &&ionSwapping) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:399: warning: Member add(TopologyData &&topologyData) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdrun/simulatorbuilder.h:404: warning: Member add(BoxDeformationHandle &&boxDeformation) (function) of class gmx::SimulatorBuilder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/basicoptionstorage.h:191: warning: Member formatSingleValue(const std::string &value) const override (function) of class gmx::StringOptionStorage is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/optionstoragetemplate.h:321: warning: Member normalizeValues(const std::vector< Any > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:158: warning: @copybrief or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/include/gromacs/utility/filestream.h:159: warning: @copydetails or @copydoc target 'TextInputFile::TextInputFile(const std::string &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/threaded_force_buffer.h:113: warning: Member processMask() (function) of class gmx::ThreadForceBuffer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:123: warning: Member update_coords(const t_inputrec &inputRecord, int64_t step, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, t_state *state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, t_fcdata *fcdata, const gmx_ekindata_t *ekind, const Matrix3x3 &parrinelloRahmanM, int UpdatePart, const t_commrec *cr, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:139: warning: Member finish_update(const t_inputrec &inputRecord, bool havePartiallyFrozenAtoms, int homenr, gmx::ArrayRef< const unsigned short > cFREEZE, t_state *state, gmx_wallcycle *wcycle, bool haveConstraints) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:147: warning: Member update_sd_second_half(const t_inputrec &inputRecord, int64_t step, real *dvdlambda, int homenr, gmx::ArrayRef< const ParticleType > ptype, gmx::ArrayRef< const real > invMass, t_state *state, const t_commrec *cr, t_nrnb *nrnb, gmx_wallcycle *wcycle, gmx::Constraints *constr, bool do_log, bool do_ene) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:161: warning: Member update_for_constraint_virial(const t_inputrec &inputRecord, int homenr, bool havePartiallyFrozenAtoms, gmx::ArrayRef< const real > invmass, gmx::ArrayRef< const gmx::RVec > invMassPerDim, const t_state &state, const gmx::ArrayRefWithPadding< const gmx::RVec > &f, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:170: warning: Member update_temperature_constants(const t_inputrec &inputRecord, const gmx_ekindata_t &ekind) (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:172: warning: Member getAndersenRandomizeGroup() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:174: warning: Member getBoltzmanFactor() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:176: warning: Member xp() (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/update.cpp:178: warning: Member deform() const (function) of class Update::Impl is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:112: warning: Member useUpdateGroups() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:113: warning: Member maxUpdateGroupRadius() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/updategroups.h:114: warning: Member updateGroupingPerMoleculeType() const (function) of class gmx::UpdateGroups is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/checkpointdata.h:412: warning: Member empty() const (function) of class gmx::WriteCheckpointDataHolder is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:169: warning: Member DonorType (enumeration) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:163: warning: Member c_maxHydrogensWithOxygen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:165: warning: Member c_maxHydrogensWithNitrogen (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:167: warning: Member c_maxHydrogenBonds (variable) of namespace gmx::analysismodules::anonymous_namespace{hbond.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/hbond.cpp:113: warning: Member HbondStorageFrame(int frnr, std::vector< HBond > data) (function) of struct gmx::analysismodules::anonymous_namespace{hbond.cpp}::HbondStorageFrame is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/msd.cpp:283: warning: Member MsdCoordinateManager(const int numAtoms, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeIndexMapping) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdCoordinateManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/msd.cpp:107: warning: Member MsdColumnProxy(std::vector< double > *column) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/msd.cpp:109: warning: Member push_back(double value) (function) of class gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/modules/msd.cpp:363: warning: Member MsdGroupData(const Selection &inputSel, ArrayRef< const MoleculeData > molecules, ArrayRef< const int > moleculeAtomMapping) (function) of struct gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdGroupData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:69: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhPointStateHistory *awhPointStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:86: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, AwhBiasStateHistory *awhBiasStateHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:100: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationBlockDataHistory *correlationBlockDataHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:121: warning: Member doCheckpoint(CheckpointData< operation > checkpointData, CorrelationGridHistory *correlationGridHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:142: warning: Member doCheckpointData(CheckpointData< operation > checkpointData, AwhBiasHistory *awhBiasHistory) (function) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/awh_history.cpp:66: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{awh_history.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:174: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/electricfield.cpp:175: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:69: warning: Member makeFepvals(const std::vector< double > &lambdaVdw, const std::vector< double > &lambdaCoul) (function) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:60: warning: Member c_numLambdas (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:62: warning: Member dhdlVdw (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:63: warning: Member dhdlCoul (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/enerdata.cpp:65: warning: Member dhdlLinearZero (variable) of namespace gmx::anonymous_namespace{enerdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/energydata.cpp:402: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{energydata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/expandedensembleelement.cpp:129: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{expandedensembleelement.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/firstorderpressurecoupling.cpp:179: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{firstorderpressurecoupling.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/freeenergyparameters.cpp:58: warning: Member lambdasAtState(const int stateIndex, gmx::ArrayRef< const std::vector< double > > lambdaArray, const int lambdaArrayExtent) (function) of namespace gmx::anonymous_namespace{freeenergyparameters.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/freeenergyperturbationdata.cpp:165: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{freeenergyperturbationdata.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp:1099: warning: Member detectCpuLimit(const std::string &root="") (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/hardwaretopology.cpp:1180: warning: Member setMaxThreads(float cpuLimit, int topologyCpus, int systemCpus) (function) of namespace gmx::anonymous_namespace{hardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxpreprocess/tests/massrepartitioning.cpp:53: warning: Member setupMTop(gmx_mtop_t *mtop, ArrayRef< const real > masses, ArrayRef< const int > bonds) (function) of namespace gmx::anonymous_namespace{massrepartitioning.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/mttk.cpp:282: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{mttk.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/neldermead.cpp:97: warning: Member defaultNelderMeadParameters (variable) of namespace gmx::anonymous_namespace{neldermead.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:294: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{parrinellorahmanbarostat.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/propagator.cpp:63: warning: Member integrationStepNames (variable) of namespace gmx::anonymous_namespace{propagator.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator/pullelement.cpp:121: warning: Member c_currentVersion (variable) of namespace gmx::anonymous_namespace{pullelement.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp:45: warning: Member Options (enumeration) of namespace gmx::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp:54: warning: Member testEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp:60: warning: Member testBoolEnumTwoIPlusJPlusK(int k) (function) of namespace gmx::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/template_mp.cpp:66: warning: Member testBoolDoubleOrNot(int k) (function) of namespace gmx::anonymous_namespace{template_mp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:194: warning: Member operator!=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() !=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:200: warning: Member operator<(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()< rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:206: warning: Member operator<=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get()<=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:212: warning: Member operator>(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() > rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:218: warning: Member operator>=(const not_null< T > &lhs, const not_null< U > &rhs) -> decltype(lhs.get() >=rhs.get()) (function) of namespace gmx::compat is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:134: warning: Member not_null(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:135: warning: Member operator=(const not_null &other)=default (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:146: warning: Member operator T() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/compat/pointers.h:147: warning: Member operator->() const (function) of class gmx::compat::not_null is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:49: warning: Member c_nBoxZ (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:50: warning: Member c_nBoxY (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:51: warning: Member c_nBoxX (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/include/gromacs/pbcutil/ishift.h:52: warning: Member c_numIvecs (variable) of namespace gmx::detail is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:484: warning: Member SimdTraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd.h:623: warning: Member Simd4TraitsT (typedef) of namespace gmx::internal is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:87: warning: Member IExceptionInfo(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:88: warning: Member IExceptionInfo(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:89: warning: Member operator=(const IExceptionInfo &)=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:90: warning: Member operator=(IExceptionInfo &&) noexcept=default (function) of class gmx::internal::IExceptionInfo is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/options/options_impl.h:200: warning: Member GMX_DISALLOW_COPY_AND_ASSIGN(OptionSectionImpl) (function) of class gmx::internal::OptionSectionImpl is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainerwithsections.h:107: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections) (function) of class gmx::IOptionsContainerWithSections is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/options/ioptionscontainer.h:143: warning: Member GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer) (function) of class gmx::IOptionsContainer is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:154: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:155: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:163: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/simd/include/gromacs/simd/simd_memory.h:164: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:72: warning: Member GpuFftTestParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:77: warning: Member GpuFftTestGridParams (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/gyrate.cpp:70: warning: Member GyrateTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/hbond.cpp:70: warning: Member HbondTestParamsMerge (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.h:60: warning: Member SimulationOptionTuple (typedef) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:79: warning: Member getGpuAwareMpiStatusForFftBackend(const FftBackend fftBackend) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gpu_utils/tests/device_availability.cpp:66: warning: Member getRequiredNumberOfDevices() (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:85: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(p) &this->mask(a)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:86: warning: Member deallocate(p, 1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:93: warning: Member v(10) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:94: warning: Member EXPECT_EQ(0, reinterpret_cast< std::size_t >(v.data()) &this->mask(v.get_allocator())) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:99: warning: Member for(std::size_t i=1000;i<=10000;i+=1000) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:125: warning: Member v1(1) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:127: warning: Member EXPECT_NE(data, nullptr) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:128: warning: Member v2(std::move(v1)) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:129: warning: Member EXPECT_EQ(data, v2.data()) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:61: warning: Member runGrompp(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:74: warning: Member runMdrun(SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:87: warning: Member compareEnergies(const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simulatorcomparison.cpp:108: warning: Member compareTrajectories(const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmegathertest.cpp:429: warning: Member registerDynamicalPmeGatherTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:414: warning: Member registerDynamicalPmeSolveTests(const Range< int > hardwareContextIndexRange) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.cpp:416: warning: Member checkTrajectoryAgainstReferenceData(const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames) (function) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:68: warning: Member g_sampleWeightCentral (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:69: warning: Member g_sampleWeightNeighbor (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:70: warning: Member g_sampleTimeStep (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/friction_metric.cpp:71: warning: Member g_numPointsPerDim (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:263: warning: Member inputGrids (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft_mpi.cpp:267: warning: Member inputBackends (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:783: warning: Member testKernelTypes (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:82: warning: Member a (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:83: warning: Member p (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/alignedallocator_impl.h:126: warning: Member data (variable) of namespace gmx::test is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/awh_setup.h:71: warning: Member AwhTestParameters(ISerializer *serializer) (function) of struct gmx::test::AwhTestParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:443: warning: @copydetails or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::GyrateInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::HbondInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/replicaexchange_equivalence.cpp:267: warning: Member operator()(const testing::TestParamInfo< ParamType > ¶meter) const (function) of struct gmx::test::PrintReplicaExchangeParametersToString is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:161: warning: Member topFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:162: warning: Member groFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:163: warning: Member mdpFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:164: warning: Member fullPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:165: warning: Member reducedPrecisionTrajectoryFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:166: warning: Member groOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:167: warning: Member cptOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:168: warning: Member ndxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:169: warning: Member mdpOutputFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:170: warning: Member tprFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:171: warning: Member logFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:172: warning: Member edrFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:173: warning: Member mtxFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:174: warning: Member swapFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:175: warning: Member dhdlFileName_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:176: warning: Member nsteps_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/moduletest.h:177: warning: Member maxwarn_ (variable) of class gmx::test::SimulationRunner is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:256: warning: Member GromacsException(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:257: warning: Member GromacsException(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:258: warning: Member operator=(const GromacsException &)=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/api/legacy/include/gromacs/utility/exceptions.h:259: warning: Member operator=(GromacsException &&) noexcept=default (function) of class gmx::GromacsException is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:73: warning: Member requestVelocities() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:74: warning: Member requestForces() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:75: warning: Member initFrameIndices(const ArrayRef< const int > &index) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:86: warning: Member initAtomTypes(const ArrayRef< const char *const > &types) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:87: warning: Member initUniformResidues(int residueSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:88: warning: Member initUniformMolecules(int moleculeSize) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:104: warning: Member setMoleculeType(int moleculeTypeIndex, ArrayRef< const int > residueSizes) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:105: warning: Member setMoleculeBlock(int moleculeBlockIndex, int moleculeTypeIndex, int numMoleculesToAdd) (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:106: warning: Member finalizeTopology() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:112: warning: Member atoms() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/tests/toputils.h:113: warning: Member frame() (function) of class gmx::test::TopologyManager is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.h:66: warning: Member coordinates (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.h:66: warning: Member velocities (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/trajectorycomparison.h:66: warning: Member forces (variable) of struct gmx::test::TrajectoryTolerances is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:140: warning: Member grid_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:141: warning: Member gridIndexToDataIndex_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:142: warning: Member data_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:143: warning: Member numColumns_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:144: warning: Member numRows_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/applied_forces/awh/tests/biasstate.cpp:145: warning: Member filename_ (variable) of class gmx::test::UserInputTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:350: warning: Member WriteFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:351: warning: Member TestFunction (typedef) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:360: warning: Member addTestValues() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:380: warning: Member test() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:354: warning: Member writeFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:356: warning: Member testFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:428: warning: Member addTestValueFunctions_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:444: warning: Member testingTypes_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:458: warning: Member fileManager_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:459: warning: Member filename_ (variable) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::CheckpointDataTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:64: warning: Member value (variable) of struct gmx::test::anonymous_namespace{checkpointdata.cpp}::IsVectorOfSerializableType is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:173: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:179: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:185: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:191: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:197: warning: Member getTestVector() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:105: warning: Member begin() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:106: warning: Member end() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:96: warning: Member Iterator(const T *ptr) (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:97: warning: Member operator++() (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:98: warning: Member operator!=(const Iterator &other) const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/checkpointdata.cpp:99: warning: Member operator*() const (function) of class gmx::test::anonymous_namespace{checkpointdata.cpp}::TestValues::TestValueGenerator::Iterator is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/cmdlinetest.cpp:254: warning: Member ViewMatchesCString(const std::string_view view) (function) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/cmdlinetest.cpp:253: warning: Member view_ (variable) of struct gmx::test::anonymous_namespace{cmdlinetest.cpp}::ViewMatchesCString is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/pbcutil/tests/com.cpp:118: warning: Member COMInPlaceTestParams (typedef) of namespace gmx::test::anonymous_namespace{com.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp:85: warning: Member c_pbcs (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdlib/tests/constr.cpp:156: warning: Member c_constraintsTestSystemList (variable) of namespace gmx::test::anonymous_namespace{constr.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/cstringutil.cpp:100: warning: Member testInplace(F f, const char *input, const char *expectedOutput) (function) of namespace gmx::test::anonymous_namespace{cstringutil.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:73: warning: Member DsspTestParamsDsspNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:74: warning: Member DsspTestParamsGromacsNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:75: warning: Member DsspTestParamsDsspNoNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/dssp.cpp:76: warning: Member DsspTestParamsGromacsNoNB (typedef) of namespace gmx::test::anonymous_namespace{dssp.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::DsspInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/exclusions.cpp:200: warning: Member testKernelTypes (variable) of namespace gmx::test::anonymous_namespace{exclusions.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/fft/tests/fft.cpp:293: warning: Member FFTTest3DParameters (typedef) of namespace gmx::test::anonymous_namespace{fft.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:73: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:74: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:76: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/fileioxdrserializer.cpp:77: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{fileioxdrserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:62: warning: Member TypeAndName (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:64: warning: Member FileTypeTestParams (typedef) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:115: warning: Member testParams (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/filetypes.cpp:124: warning: Member prefixes (variable) of namespace gmx::test::anonymous_namespace{filetypes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp:72: warning: Member ListOfInteractionsToTest (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/freeenergy.cpp:73: warning: Member FreeEnergyReferenceTestParams (typedef) of namespace gmx::test::anonymous_namespace{freeenergy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:67: warning: Member checkIndexGroup(TestReferenceChecker *checker, const IndexGroup &group) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:74: warning: Member checkBlocks(TestReferenceChecker *checker, ArrayRef< const IndexGroup > blocks) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:81: warning: Member compareBlocks(ArrayRef< const IndexGroup > one, ArrayRef< const IndexGroup > two) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/topology/tests/index.cpp:95: warning: Member checkFileMatch(TestReferenceChecker *checker, const std::string &fileName, const std::string &fullPath) (function) of namespace gmx::test::anonymous_namespace{index.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:70: warning: Member c_int16ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:71: warning: Member c_int32Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:72: warning: Member c_int32ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:73: warning: Member c_int64Value (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:74: warning: Member c_int64ValueSwapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:76: warning: Member c_intAndFloat32 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:77: warning: Member c_intAndFloat64 (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:79: warning: Member c_intAndFloat32Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/utility/tests/inmemoryserializer.cpp:80: warning: Member c_intAndFloat64Swapped (variable) of namespace gmx::test::anonymous_namespace{inmemoryserializer.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:505: warning: Member isTabulated(const CoulombKernelType coulombKernelType) (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:530: warning: Member makeRefDataFileName() (function) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:203: warning: Member c_numEnergyGroups (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:461: warning: Member coulombKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:467: warning: Member vdwKernelTypeName (variable) of namespace gmx::test::anonymous_namespace{kernel_test.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:374: warning: Member TupleT (typedef) of struct gmx::test::anonymous_namespace{kernel_test.cpp}::KernelInputParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:381: warning: Member KernelInputParameters(TupleT t) (function) of struct gmx::test::anonymous_namespace{kernel_test.cpp}::KernelInputParameters is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:391: warning: Member NbnxmKernelTest(LJCombinationRule ljCombinationRule) (function) of class gmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:393: warning: Member options_ (variable) of class gmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:394: warning: Member system_ (variable) of class gmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/tests/kernel_test.cpp:395: warning: Member nbv_ (variable) of class gmx::test::anonymous_namespace{kernel_test.cpp}::NbnxmKernelTest is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:170: warning: Member minimizersToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:172: warning: Member constrainedSystemsToTest_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/minimize.cpp:175: warning: Member minimizersToTestWithConstraints_g (variable) of namespace gmx::test::anonymous_namespace{minimize.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp:162: warning: Member checkHardwareTopology(TestReferenceChecker *checker, const HardwareTopology &hwTop) (function) of namespace gmx::test::anonymous_namespace{mockhardwaretopology.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/hardware/tests/mockhardwaretopology.cpp:256: warning: Member runTest(const HardwareTopology &hwTop) (function) of class gmx::test::anonymous_namespace{mockhardwaretopology.cpp}::MockHardwareTopologyTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/mdtypes/tests/multipletimestepping.cpp:139: warning: Member simpleMtsOpts() (function) of namespace gmx::test::anonymous_namespace{multipletimestepping.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:97: warning: Member c_numAtomTypes (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:511: warning: Member c_softcoreBeutlerAlphaOrGapsysLinpointScaling (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:512: warning: Member c_softcoreCoulomb (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:513: warning: Member c_softcoreType (variable) of namespace gmx::test::anonymous_namespace{nb_free_energy.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:349: warning: Member getNbList() (function) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:331: warning: Member idef (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:334: warning: Member chargeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:335: warning: Member chargeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:336: warning: Member typeA (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:337: warning: Member typeB (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:341: warning: Member iAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:342: warning: Member jAtoms (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:343: warning: Member jIndex (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:344: warning: Member shift (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:345: warning: Member gid (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp:346: warning: Member exclFep (variable) of struct gmx::test::anonymous_namespace{nb_free_energy.cpp}::AtomData is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/normalmodes.cpp:168: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(NormalModesTest) (function) of namespace gmx::test::anonymous_namespace{normalmodes.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/math/tests/optimization.cpp:60: warning: Member mcCormick(ArrayRef< const real > x) (function) of namespace gmx::test::anonymous_namespace{optimization.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp:200: warning: Member frHelper (variable) of namespace gmx::test::anonymous_namespace{pairs.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/pairs.cpp:102: warning: Member OutputQuantities(int energyGroup) (function) of struct gmx::test::anonymous_namespace{pairs.cpp}::OutputQuantities is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:108: warning: Member enumValueToString(PmeSolveAlgorithm enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesolvetest.cpp:115: warning: Member enumValueToString(GridOrdering enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesolvetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:173: warning: Member enumValueToString(SplineAndSpreadOptions enumValue) (function) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:85: warning: Member c_testSystems (variable) of namespace gmx::test::anonymous_namespace{pmesplinespreadtest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp:96: warning: Member PmeTestParameters (typedef) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pmetest.cpp:404: warning: Member c_reproducesEnergies (variable) of namespace gmx::test::anonymous_namespace{pmetest.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/listed_forces/tests/position_restraints.cpp:148: warning: Member c_emptyLambdas (variable) of namespace gmx::test::anonymous_namespace{position_restraints.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp:173: warning: Member isTransformationPullSetup(const std::string &pullSetupName) (function) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/pull.cpp:79: warning: Member c_mdpPullParams (variable) of namespace gmx::test::anonymous_namespace{pull.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:95: warning: Member getCDataChildNode(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:105: warning: Member hasCDataContent(XMLNodePtr node) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:333: warning: Member createElementAndContents(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:246: warning: Member setIdAttribute(XMLElementPtr element, const std::string &id) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:254: warning: Member createElement(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:262: warning: Member createChildElements(XMLElementPtr parentElement, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:304: warning: Member createElementContents(XMLElementPtr element, const ReferenceDataEntry &entry) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/refdata_xml.cpp:339: warning: Member createRootElement(XMLDocumentPtr document) (function) of namespace gmx::test::anonymous_namespace{refdata_xml.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/rerun.cpp:111: warning: Member executeRerunTest(TestFileManager *fileManager, SimulationRunner *runner, const std::string &simulationName, int numWarningsToTolerate, const MdpFieldValues &mdpFieldValues, const EnergyTermsToCompare &energyTermsToCompare, const TrajectoryComparison &trajectoryComparison) (function) of namespace gmx::test::anonymous_namespace{rerun.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/scattering.cpp:68: warning: Member ScatteringTestDirectModeParams (typedef) of namespace gmx::test::anonymous_namespace{scattering.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/testutils/include/testutils/cmdlinetest.h:442: warning: @copybrief or @copydoc target 'setOutputFile(const char *, const ITextBlockMatcherSettings &)' not found /build/reproducible-path/gromacs-2024.4/src/gromacs/trajectoryanalysis/tests/moduletest.h:200: warning: Member createModule() override (function) of class TrajectoryAnalysisModuleTestFixture< gmx::analysismodules::ScatteringInfo > is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/simple_mdrun.cpp:191: warning: Member GTEST_ALLOW_UNINSTANTIATED_PARAMETERIZED_TEST(SimpleMdrunTest) (function) of namespace gmx::test::anonymous_namespace{simple_mdrun.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests/timing.cpp:75: warning: Member delayInMilliseconds (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/timing/tests/timing.cpp:76: warning: Member wcycle (variable) of class gmx::test::anonymous_namespace{timing.cpp}::TimingTest is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/tools/tests/trjconv.cpp:155: warning: Member DumpTestParameters (typedef) of namespace gmx::test::anonymous_namespace{trjconv.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/programs/mdrun/tests/virtualsites.cpp:86: warning: Member VirtualSiteTestParams (typedef) of namespace gmx::test::anonymous_namespace{virtualsites.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/fileio/tests/xvgio.cpp:63: warning: Member compareValues(basic_mdspan< const double, dynamicExtents2D > ref, basic_mdspan< const double, dynamicExtents2D > test) (function) of namespace gmx::test::anonymous_namespace{xvgio.cpp} is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:125: warning: Member mode (typedef) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/grid.cpp:122: warning: Member getMaxNumCells(const Grid::Geometry &geometry, const int numAtoms, const int numColumns) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gridset.cpp:135: warning: Member getGridOffset(gmx::ArrayRef< const Grid > grids, int gridIndex) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_buffer_ops.cpp:63: warning: Member nbnxn_gpu_x_to_nbat_x(const Nbnxm::Grid &grid, NbnxmGpu *nb, DeviceBuffer< gmx::RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const gmx::AtomLocality locality, int gridId, int numColumnsMax, bool mustInsertNonLocalDependency) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:83: warning: Member init_ewald_coulomb_force_table(const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:97: warning: Member useTabulatedEwaldByDefault(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:128: warning: Member nbnxn_gpu_pick_ewald_kernel_type(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:178: warning: Member set_cutoff_parameters(NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:202: warning: Member initPlistSorting(gpuPlistSorting *sorting) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:225: warning: Member init_plist(gpu_plist *pl) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:253: warning: Member init_timings(gmx_wallclock_gpu_nbnxn_t *t) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:302: warning: Member nbnxmGpuPickVdwKernelType(const interaction_const_t &ic, LJCombinationRule ljCombinationRule) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:356: warning: Member nbnxmGpuPickElectrostaticsKernelType(const interaction_const_t &ic, const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:442: warning: Member gpu_init(const gmx::DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxn_atomdata_t *nbat, const bool bLocalAndNonlocal) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:511: warning: Member gpu_pme_loadbal_update_param(nonbonded_verlet_t *nbv, const interaction_const_t &ic) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:528: warning: Member gpu_upload_shiftvec(NbnxmGpu *nb, const nbnxn_atomdata_t *nbatom) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:689: warning: Member gpu_init_atomdata(NbnxmGpu *nb, const nbnxn_atomdata_t *nbat) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:792: warning: Member gpu_clear_outputs(NbnxmGpu *nb, bool computeVirial) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:823: warning: Member gpu_is_kernel_ewald_analytical(const NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:829: warning: Member setupGpuShortRangeWork(NbnxmGpu *nb, const gmx::ListedForcesGpu *listedForcesGpu, const gmx::InteractionLocality iLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:842: warning: Member haveGpuShortRangeWork(const NbnxmGpu *nb, const gmx::InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:981: warning: Member nbnxnInsertNonlocalGpuDependency(NbnxmGpu *nb, const InteractionLocality interactionLocality) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1076: warning: Member nbnxn_gpu_init_x_to_nbat_x(const Nbnxm::GridSet &gridSet, NbnxmGpu *gpu_nbv) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1286: warning: Member gpuGetNBAtomData(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp:1292: warning: Member gpu_get_f(NbnxmGpu *nb) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/nbnxm_setup.cpp:355: warning: Member getENbnxnInitCombRule(const t_forcerec &forcerec) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel.cpp:53: warning: Member getNbnxmSubGroupSize(const DeviceInformation &deviceInfo) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:1455: warning: Member launchNbnxmKernelHelper(NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc) (function) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:106: warning: Member elecEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:109: warning: Member elecEwaldTab (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/sycl/nbnxm_sycl_kernel_body.h:112: warning: Member ljEwald (variable) of namespace Nbnxm is not documented. /build/reproducible-path/gromacs-2024.4/src/gromacs/nbnxm/gpu_types_common.h:276: warning: Member scanTemporary (variable) of struct Nbnxm::gpuPlistSorting is not documented. /build/reproducible-path/gromacs-2024.4/docs/doxygen/directories.cpp:96: warning: unable to resolve reference to 'sm_insolidangle' for \ref command /build/reproducible-path/gromacs-2024.4/src/gromacs/selection/sm_insolidangle.cpp:99: warning: unable to resolve reference to 'sm_insolidangle' for \ref command cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/doxygen-full-timestamp.txt make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-full /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen /build/reproducible-path/gromacs-2024.4/build/documentation/docs/doxygen/CMakeFiles/doxygen-all.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[4]: Nothing to be done for 'docs/doxygen/CMakeFiles/doxygen-all.dir/build'. make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target doxygen-all /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/depend make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/docs /build/reproducible-path/gromacs-2024.4/build/documentation /build/reproducible-path/gromacs-2024.4/build/documentation/docs /build/reproducible-path/gromacs-2024.4/build/documentation/docs/CMakeFiles/webpage.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/build make[4]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/documentation' cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E remove -f /build/reproducible-path/gromacs-2024.4/build/documentation/docs/html/manual-2024.4-Debian_2024.4_1.pdf cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E copy /build/reproducible-path/gromacs-2024.4/build/documentation/docs/manual/gromacs.pdf /build/reproducible-path/gromacs-2024.4/build/documentation/docs/html/manual-2024.4-Debian_2024.4_1.pdf cd /build/reproducible-path/gromacs-2024.4/build/documentation/docs && /usr/bin/cmake -E echo "Webpage output: file:///build/reproducible-path/gromacs-2024.4/build/documentation/docs/html/index.html" Webpage output: file:///build/reproducible-path/gromacs-2024.4/build/documentation/docs/html/index.html make[4]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' [100%] Built target webpage make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/documentation' touch build-manual dh_testdir dh_testroot dh_prep dh_installdirs /usr/bin/make -j12 -C build/mpi install DESTDIR=/build/reproducible-path/gromacs-2024.4/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -P /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/mpi//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/mpi/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 0%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 2%] Built target thread_mpi [ 4%] Built target tng_io_obj /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/colvars_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 4%] Built target lmfit_objlib /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend [ 4%] Built target release-version-info [ 8%] Built target colvars_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 8%] Built target linearalgebra [ 8%] Built target options [ 8%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" [ 8%] Built target gmx_objlib [ 8%] Built target energyanalysis make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 8%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build [ 8%] Built target taskassignment make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 11%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target libgromacs /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/depend /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/api/gmxapi/CMakeFiles/gmxapi.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/gmxapi/CMakeFiles/gmxapi.dir/build.make api/gmxapi/CMakeFiles/gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [ 95%] Built target gmxapi /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/DependInfo.cmake "--color=" /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/depend [ 97%] Built target nblib make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/DependInfo.cmake "--color=" [ 97%] Built target gmx /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi/api/nblib/samples/CMakeFiles/methane-water-integration.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_resources.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build [100%] Built target gmxapi_extension_resources make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target argon-forces-integration /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/depend /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/DependInfo.cmake "--color=" [100%] Built target methane-water-integration make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build.make python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/gmxapi/CMakeFiles/_gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_ensemblepotential.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build.make python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/cpp/CMakeFiles/gmxapi_extension_test.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target _gmxapi [100%] Built target gmxapi_extension_ensemblepotential [100%] Built target gmxapi_extension_test /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' cd /build/reproducible-path/gromacs-2024.4/build/mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2024.4/build/mpi /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule /build/reproducible-path/gromacs-2024.4/build/mpi/python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -f python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build.make python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[3]: Nothing to be done for 'python_packaging/sample_restraint/src/pythonmodule/CMakeFiles/gmxapi_extension.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' [100%] Built target gmxapi_extension make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README.tutor -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/export.dlg -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc216.gro -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sw.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.dtd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/cb-shift.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atom_nom.tbl -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/surface.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ps.m2p -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atommass.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/elements.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/random.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Installing: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ss.map -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/README -- Installing: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_mpi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-gmx_mpi.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Installing: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-order.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Installing: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Installing: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-help.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi' /usr/bin/make -j12 -C build/mpi-dp install DESTDIR=/build/reproducible-path/gromacs-2024.4/debian/tmp make[1]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/cmake -S/build/reproducible-path/gromacs-2024.4 -B/build/reproducible-path/gromacs-2024.4/build/mpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi-dp/CMakeFiles /build/reproducible-path/gromacs-2024.4/build/mpi-dp//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/mpi-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/mpi-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake "--color=" [ 0%] Built target scanner make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build [ 0%] Built target release-version-info make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build [ 2%] Built target thread_mpi make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/depend [ 4%] Built target tng_io_obj /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" [ 4%] Built target lmfit_objlib make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/depend /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 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'/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/pulling/CMakeFiles/pulling.dir/build.make src/gromacs/pulling/CMakeFiles/pulling.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'src/gromacs/pulling/CMakeFiles/pulling.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 6%] Built target energyanalysis [ 6%] Built target gmx_objlib [ 8%] Built target options make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/colvars_objlib.dir/build.make src/gromacs/CMakeFiles/colvars_objlib.dir/build [ 10%] Built target pulling /usr/bin/make -f src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/build.make src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/depend [ 10%] Built target mdrun_objlib /usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/taskassignment/CMakeFiles/taskassignment.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator /build/reproducible-path/gromacs-2024.4/build/mpi-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake "--color=" make[3]: Entering directory 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'/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'api/gmxapi/CMakeFiles/gmxapi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[3]: Nothing to be done for 'api/nblib/CMakeFiles/nblib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [ 97%] Built target nblib /usr/bin/make -f api/nblib/samples/CMakeFiles/argon-forces-integration.dir/build.make api/nblib/samples/CMakeFiles/argon-forces-integration.dir/depend [100%] Built target gmxapi make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" /usr/bin/make -f api/nblib/samples/CMakeFiles/methane-water-integration.dir/build.make api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' cd /build/reproducible-path/gromacs-2024.4/build/mpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/mpi-dp /build/reproducible-path/gromacs-2024.4/build/mpi-dp/api/nblib/samples 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make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/mpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/mpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so.9.0.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so.9 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_mpi_d.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_mpi_d.pc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs_mpi_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_mpi_d/gromacs-hints_mpi_d.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_mpi_d -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-gmx_mpi_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dipoles.1 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"--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/CMakeFiles/nblib.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/make -f api/nblib/CMakeFiles/nblib.dir/build.make api/nblib/CMakeFiles/nblib.dir/build make[3]: Leaving directory 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api/nblib/samples/CMakeFiles/methane-water-integration.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic/api/nblib/samples/CMakeFiles/argon-forces-integration.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' cd /build/reproducible-path/gromacs-2024.4/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib/samples /build/reproducible-path/gromacs-2024.4/build/basic 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'/build/reproducible-path/gromacs-2024.4/build/basic' make[3]: Nothing to be done for 'api/nblib/samples/CMakeFiles/methane-water-integration.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' [ 98%] Built target argon-forces-integration [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/template/CMakeLists.txt -- Installing: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/vdwradii.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.dtd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/vdw-msms.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/random.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber94.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a6.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ca-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/spc.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG45a3.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ss.map -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/README -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx.pl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectory -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectory/trajectoryframe.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/idef.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/atoms.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/topology_enums.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/block.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/atomprop.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/ifunc.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/topology.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/index.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/symtab.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/topology/forcefieldparameters.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/programcontext.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/range.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/flags.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/classhelpers.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/arrayref.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/stringutil.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/fileptr.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/listoflists.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/pleasecite.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/exceptions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/smalloc.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/unique_cptr.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/real.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/current_function.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/enumerationhelpers.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/futil.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/baseversion.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/arraydata.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/abstractdata.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/dataframe.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/displacement.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/lifetime.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/plot.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/modules/average.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/analysisdata/analysisdata.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/pbcutil -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/pbcutil/pbc.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectionoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectioncollection.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/indexutil.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selection.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectionenums.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectionoption.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/nbsearch.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/selectionoptionbehavior.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/selection/position.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/vec.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/do_fit.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/units.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/vectypes.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/functions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/math/utilities.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/ivaluestore.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/optionfiletype.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/filenameoptionmanager.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/ioptionsbehavior.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/timeunitmanager.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/filenameoption.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/optionflags.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/basicoptions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/abstractoption.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/options.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/options/ioptionscontainer.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdtypes -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdtypes/md_enums.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdtypes/inputrec.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/confio.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/trxio.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/filetypes.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/oenv.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/fileio/tpxio.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/restraint -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/restraint/restraintpotential.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/version.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/libgromacs_export.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/kerneloptions.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/fwd.hpp -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/external/boost/stl_interfaces/iterator_interface.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so.9.0.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so.9 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs.pc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/gromacs-config.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/gromacs-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs/gromacs-hints.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-gmx.bash -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: 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src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend /usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd 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/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/CMakeFiles/colvars_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4 && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2024.4-Debian_2024.4_1 -D PROJECT_SOURCE_DIR=/build/reproducible-path/gromacs-2024.4 -D VERSION_CMAKEIN=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/build/reproducible-path/gromacs-2024.4/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Debian-2024.4-1 -P /build/reproducible-path/gromacs-2024.4/cmake/gmxGenerateVersionInfoWithoutGit.cmake make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: 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"--color=" [ 5%] Built target lmfit_objlib [ 5%] Built target release-version-info /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/depend [ 9%] Built target colvars_objlib make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/options/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/options/CMakeFiles/options.dir/build.make src/gromacs/options/CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/CMakeFiles/gmx_objlib.dir/DependInfo.cmake "--color=" /usr/bin/make -f src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build.make src/gromacs/energyanalysis/CMakeFiles/energyanalysis.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/options/CMakeFiles/options.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' [ 9%] Built target linearalgebra make[3]: Entering directory 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/usr/bin/make -f src/programs/CMakeFiles/gmx_objlib.dir/build.make src/programs/CMakeFiles/gmx_objlib.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/pulling/CMakeFiles/pulling.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx_objlib.dir/build'. make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' 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target taskassignment [ 15%] Built target modularsimulator /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[3]: Nothing to 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make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs /build/reproducible-path/gromacs-2024.4/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' cd /build/reproducible-path/gromacs-2024.4/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gromacs-2024.4 /build/reproducible-path/gromacs-2024.4/api/nblib /build/reproducible-path/gromacs-2024.4/build/basic-dp /build/reproducible-path/gromacs-2024.4/build/basic-dp/api/nblib 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argon-forces-integration [100%] Built target methane-water-integration make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gromacs-2024.4/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README.tutor -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/README_FreeEnergyModifications.txt -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/scatteringfactors.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/co-shift.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/dgsolv.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber96.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/spce.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffoplsaa-n.tst -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexspc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/bonds.dlg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/urea.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/amber99sb.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a1.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/refi_aa.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG43a2.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Up-to-date: 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Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/specbond.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: 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/build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/phbres.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-8.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/nsfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/sfactor.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/ffG53a5.itp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/tip4p.gro -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-11.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/table6-12.xvg -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/gromacs/top/residuetypes.dat -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.zsh -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/GMXRC.csh -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux.pl -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx.pl -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so.0.4.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgmxapi_d.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gmxapi/gmxapi-config.cmake -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapicompat.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/gmxapi_mpi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdsignals.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md/mdmodule.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/exceptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/mdparams.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/compat/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/context.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gmxapi.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/session/resources.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/md.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/status.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/gromacsfwd.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/system.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/version.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gmxapi/mpi/resourceassignment.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0.1.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so.0 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libnblib_gmx.so -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/box.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/simulationstate.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particlesequencer.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/basicdefinitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/definitions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/calculator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/listed_forces/bondtypes.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/exception.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nbnxmsetuphelpers.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/particletype.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/molecules.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/nblib.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/interactions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/vector.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/traits.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/setup.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/util/util.hpp -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/tpr.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/topology.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/gmxcalculatorcpu.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/integrator.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/nblib/kerneloptions.h -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/include/gromacs/mdrun/simulationinputhandle.h -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so.9.0.0 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so.9 -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/libgromacs_d.so -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_d.pc -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/libgromacs.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/libgromacs-release.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/gromacs_d-config-version.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/cmake/gromacs_d/gromacs-hints_d.cmake -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_d -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash -- Installing: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-gmx_d.bash -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-disre.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-solvate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-msd.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-scattering.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hydorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helixorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-helix.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gyrate-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-lie.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-make_edi.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-xpm2ps.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nonbonded-benchmark.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-report-methods.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-nmens.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-tune_pme.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trajectory.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-wham.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sorient.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-editconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mdrun.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hbond-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-trjconv.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rms.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-convert-trj.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-dssp.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-extract-cluster.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-grompp.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sans-legacy.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/share/man/man1/gmx-saxs-legacy.1 make[1]: Leaving directory '/build/reproducible-path/gromacs-2024.4/build/basic-dp' chrpath -d /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_mpi /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx_mpi_d chrpath -d /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/lib/*/libgromacs_mpi*.so.* perl -lne 'print' /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion.bash \ /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-*.bash > \ /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/gmx-completion-concat mv /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux.pl /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/demux mv /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx.pl /build/reproducible-path/gromacs-2024.4/debian/tmp/usr/bin/xplor2gmx dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_bash-completion -a dh_lintian -a dh_link -a dh_testdir -i dh_testroot -i dh_installdirs -i dh_install -i dh_installdocs -i dh_installchangelogs -i dh_installman -i find /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/ -type f -a \( -name '*.md5' -o -name '*.map' \) -delete rdfind -outputname /dev/null -makesymlinks true /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/ Now scanning "/build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc", found 23450 files. Now have 23450 files in total. Removed 0 files due to nonunique device and inode. Total size is 376902055 bytes or 359 MiB Removed 7953 files due to unique sizes from list. 15497 files left. Now eliminating candidates based on first bytes: removed 3350 files from list. 12147 files left. Now eliminating candidates based on last bytes: removed 1749 files from list. 10398 files left. Now eliminating candidates based on sha1 checksum: removed 3288 files from list. 7110 files left. It seems like you have 7110 files that are not unique Totally, 23 MiB can be reduced. Now making results file /dev/null Now making symbolic links. creating Making 4129 links. symlinks -r -s -c /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/ absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/jquery.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> ../html-full/jquery.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/template_8cpp__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> ../html-full/template_8cpp__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000021_000002.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000021_000002.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000021_000002.xhtml -> ../html-lib/dir_000021_000002.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.css -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doxygen.css changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.css -> ../html-full/doxygen.css absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000085_000002.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000086_000002.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000085_000002.xhtml -> ../html-lib/dir_000086_000002.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputadapters_8h__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputadapters_8h__incl.svg -> ../html-full/outputadapters_8h__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000065_000002.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000066_000002.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000065_000002.xhtml -> ../html-lib/dir_000066_000002.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/state_8h__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/state_8h__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/state_8h__incl.svg -> ../html-full/state_8h__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPointSetRef.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataPointSetRef.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000148_000002.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000149_000002.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000148_000002.xhtml -> ../html-lib/dir_000149_000002.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextLineWrapper.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper.xhtml -> ../html-lib/classgmx_1_1TextLineWrapper.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hostallocator_8h__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hostallocator_8h__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hostallocator_8h__incl.svg -> ../html-full/hostallocator_8h__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/gammadistribution_8h__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/gammadistribution_8h__incl.svg -> ../html-full/gammadistribution_8h__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h__incl.svg -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/outputselector_8h__incl.svg changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/outputselector_8h__incl.svg -> ../html-full/outputselector_8h__incl.svg absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000002.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000009_000002.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000009_000002.xhtml -> ../html-lib/dir_000009_000002.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution.xhtml absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution.xhtml -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution.xhtml changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution.xhtml -> 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/build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_13.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/enums_13.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/enums_13.js -> ../../html-full/search/enums_13.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/related_0.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/search/related_1.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/related_0.js -> ../../html-lib/search/related_1.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/search/pages_9.js -> 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/build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_1b.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/all_1e.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_1b.js -> all_1e.js absolute: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_0.js -> /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/all_2.js changed: /build/reproducible-path/gromacs-2024.4/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_0.js -> all_2.js dh_bash-completion -i dh_lintian -i dh_link -i dh_strip_nondeterminism -i dh_compress -i -X.pdf dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'gromacs-data' in '../gromacs-data_2024.4-1_all.deb'. dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -A dh_makeshlibs -a dh_shlibdeps -plibgromacs9 -L libgromacs9 -l debian/libgromacs9/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_shlibdeps -plibnblib-gmx0 -L libnblib-gmx0 -l debian/libnblib-gmx0/usr/lib:debian/libgromacs9/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_shlibdeps -pgromacs -L libgromacs9 -l debian/libgromacs9/usr/lib:debian/gromacs/usr/lib dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libnblib-gmx-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2024.4-1_arm64.deb'. dpkg-deb: building package 'libgromacs9-dbgsym' in '../libgromacs9-dbgsym_2024.4-1_arm64.deb'. dpkg-deb: building package 'libnblib-gmx0' in '../libnblib-gmx0_2024.4-1_arm64.deb'. dpkg-deb: building package 'libgromacs9' in '../libgromacs9_2024.4-1_arm64.deb'. dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2024.4-1_arm64.deb'. dpkg-deb: building package 'gromacs' in '../gromacs_2024.4-1_arm64.deb'. dpkg-deb: building package 'libnblib-gmx-dev' in '../libnblib-gmx-dev_2024.4-1_arm64.deb'. dpkg-deb: building package 'libnblib-gmx0-dbgsym' in '../libnblib-gmx0-dbgsym_2024.4-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../gromacs_2024.4-1_arm64.buildinfo dpkg-genchanges --build=binary -O../gromacs_2024.4-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1219924/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1219924/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1219924 and its subdirectories I: Current time: Mon Dec 2 02:39:13 +14 2024 I: pbuilder-time-stamp: 1733056753